Same Office Action, Different Stakes: Responding to USPTO Office Actions in Ex Parte Reexamination and Ordinary Patent Prosecution

Executive Summary: This article explains why responding to an Office Action in ex parte reexamination requires a different strategy than responding during ordinary patent prosecution. In ordinary prosecution, the applicant is generally trying to obtain commercially useful claim scope and may have procedural flexibility through amendment, RCE practice, or continuation practice. In reexamination, by contrast, the patent owner is defending issued rights—often in parallel with litigation—and should treat the first non-final Office Action response as a critical merits record for allowance, appeal, and later enforcement. The article emphasizes that patent owners should make all available arguments early, separately argue meaningful dependent claims to preserve fallback positions for appeal, and avoid reflexive amendments because amended or new reexamination claims can create intervening-rights, damages, infringement, and claim-construction consequences. It also explains that litigation counsel and reexamination counsel must coordinate before any narrowing position is taken, because even arguments that do not create statutory intervening rights under Marine Polymer may still affect claim construction, prosecution disclaimer, and litigation strategy. Finally, the article highlights that reexamination appeals from the Central Reexamination Unit (CRU) are handled with special dispatch, so appeal should refine a record built before the examiner rather than attempt to create that record for the first time.

I.             Introduction

At first glance, a response to an Office Action in ex parte reexamination looks familiar to any patent prosecutor. The patent owner receives an Office Action, analyzes rejections, considers amendments, prepares remarks, and, if necessary, appeals to the Patent Trial and Appeal Board. Those mechanics resemble ordinary prosecution of a pending patent application. But the resemblance is misleading. In ordinary prosecution, the applicant is trying to obtain a patent. In reexamination, the patent owner is trying to preserve an already-issued patent, often while the patent is being asserted in district court or used in licensing negotiations.

That difference changes the entire response strategy. A prosecution response can often be iterative. A reexamination response should be defensive, record-conscious, appeal-conscious, and, where litigation is pending, generally amendment-averse. In reexamination, the patent owner should assume that the response to the first non-final Office Action may be the principal opportunity to present all claim-construction arguments, all prior-art distinctions, all dependent-claim fallback positions, and all supporting evidence. See 37 C.F.R. § 1.111(b), (c); MPEP § 2271; MPEP § 2272.

II.          Different Procedural Posture, Different Objective

Ordinary patent prosecution concerns a pending application. The applicant has not yet obtained enforceable patent rights and is generally trying to secure commercially useful claim scope. The applicant may respond to a non-final Office Action with argument, amendment, evidence, or some combination of those tools. See 37 C.F.R. § 1.111. If prosecution later closes, the applicant may often file a request for continued examination, pursue continuation practice, or otherwise continue shaping the claim set. See 37 C.F.R. § 1.114(a), (c), (d).

Ex parte reexamination is different. It concerns an issued patent. Subject to applicable AIA estoppel provisions, a request for ex parte reexamination may be filed by “any person” during the patent’s enforceability period and is based on prior art cited under 35 U.S.C. § 301. See 35 U.S.C. § 302.The Director must determine, within three months of the request, whether the request raises a substantial new question of patentability. 35 U.S.C. § 303(a).

Once reexamination is ordered, the proceeding is not a clean continuation of ordinary prosecution. It is a post-issuance validity proceeding conducted inside the USPTO, typically handled through the Central Reexamination Unit and subject to the statutory command of “special dispatch.” See 35 U.S.C. § 305; MPEP § 2236; MPEP § 2261. Critically, that special-dispatch requirement expressly extends to “any appeal to the Patent Trial and Appeal Board.” 35 U.S.C. § 305.

The client objective also changes. In ordinary prosecution, the goal is to obtain allowable claim scope. In reexamination, the goal is to preserve enforceable claim scope. That distinction matters most when the patent is in litigation. A claim that survives reexamination only through amendment may be less valuable than a narrower dependent claim that survives as issued. The response strategy should therefore begin with a simple but important question: is the patent owner trying to obtain claims, or preserve damages-bearing claims?

III.      Reexamination Is Narrower in Scope, But Not Lower Stakes

Ordinary prosecution can involve the full range of patentability and formal issues: novelty, obviousness, eligibility, written description, enablement, indefiniteness, double patenting, restriction practice, drawings, inventorship, and information-disclosure issues.

By contrast, ex parte reexamination ordered under 35 U.S.C. § 304 is focused principally on patents and printed publications. The MPEP states that claims in an ex parte reexamination are examined on the basis of patents or printed publications, and that § 112 issues are addressed only with respect to new claims or amendatory subject matter. 37 C.F.R. § 1.552(a); MPEP § 2258. Reexamination is therefore narrower than ordinary prosecution, but the stakes are often higher because the claims already exist as enforceable property rights.

This narrower scope should influence the response. A reexamination response should not read like a broad prosecution essay about the invention. It should be tightly tied to the ordered substantial new question of patentability and the specific prior art patents and printed publications applied by the examiner. When litigation is pending, unnecessary characterizations of “the invention” can be used later in claim construction, noninfringement, prosecution disclaimer, or damages arguments. The best reexamination responses are therefore often narrower, more disciplined, and more claim-specific than ordinary prosecution responses.

IV.       The Non-Final Response Is the Main Event

The most important practical difference is timing. In ordinary prosecution, the applicant may have meaningful procedural room after a non-final response. The applicant may receive another non-final action, may file an RCE after final, may pursue continuation practice, or may refine the claim strategy over time. See 37 C.F.R. § 1.114.

In ex parte reexamination, there is also a post-order patent-owner statement procedure that should not be confused with the later response to an Office Action. After reexamination is ordered, the patent owner may file a statement, including any proposed narrowing amendments, within the period set by the Office. See 37 C.F.R. § 1.530; MPEP § 2249. The patent owner may also waive that statement, in which case the proceeding may move more directly to the first Office Action. See MPEP § 2249. Either way, once an Office Action issues, the patent owner’s response must be drafted with the constraints of reexamination practice in mind.

In responding to that Office Action, the patent owner should not count on the same flexibility available in ordinary prosecution. MPEP § 2271 states that the patent owner’s statement and response to the first Office Action “should completely respond to and/or amend with a view to avoiding all outstanding grounds of rejection,” and that the second Office Action following the order for reexamination will generally be made final. MPEP § 2271.

After final rejection, the patent owner’s position becomes much more constrained. MPEP § 2272 explains that prosecution before the examiner is intended to conclude with final action; once a non-premature final rejection is entered, the patent owner no longer has a right to unrestricted further prosecution. MPEP § 2272. The same section specifically emphasizes that there is no opportunity to refile under 37 C.F.R. § 1.53 and no opportunity to file an RCE under 37 C.F.R. § 1.114 in reexamination. Id.; see also 37 C.F.R. § 1.114(e)(6).

The result is a different drafting discipline. A reexamination response to a non-final Office Action should be treated less like an opening negotiation and more like the foundation for allowance, after-final practice, appeal, and later enforcement. The response should address every ground of rejection, identify each claim or claim group being argued, present the patentable distinctions over the applied references, and include available evidence. See 37 C.F.R. § 1.111(b), (c); MPEP § 2266; MPEP § 2272.

This is not merely good drafting hygiene. It is preservation. Section 1.111 requires the applicant or patent owner to “distinctly and specifically” point out the supposed errors in the examiner’s action, reply to every ground of objection and rejection, and present the specific distinctions believed to render the claims patentable over the applied references. 37 C.F.R. § 1.111(b), (c). A general statement that the claims are patentable is not enough. Id.

V.          Dependent Claims Should Be Argued as Appeal-Preservation Assets

Dependent claims are often treated casually in ordinary prosecution. A response may focus

on the independent claims, with the dependent claims standing or falling with them unless a particular dependent limitation becomes important. That approach is risky in reexamination.

In reexamination, dependent claims may be the patent owner’s best fallback position. They may contain narrower limitations that avoid the cited art while preserving issued claim language. When the patent is in litigation, that distinction is crucial: an already-issued dependent claim may preserve enforceable scope without the intervening-rights and damages problems that can arise from amending an independent claim.

For that reason, meaningful dependent claims should be separately argued in the response to the non-final Office Action. The response should not simply state that “the dependent claims are patentable for at least the same reasons as the independent claims.” That language may be adequate where no separate dependent-claim issue is intended, but it does little to preserve a fallback position. A stronger reexamination response identifies the specific dependent limitation, explains where the examiner’s cited art fails to disclose or suggest it, and ties the argument to the precise ground of rejection.

This approach also matters on appeal. Under 37 C.F.R. § 41.37(c)(1)(iv), each contested ground of rejection must be argued under a separate heading, and claims subject to the same ground may be argued separately, as a group, or as subgroups. If claims are argued as a group or subgroup, the Board may select a single representative claim and decide the rejection for the group based on that claim alone. 37 C.F.R. § 41.37(c)(1)(iv). The failure to separately argue grouped claims waives the argument that the Board must consider their patentability separately. Id.; MPEP § 1205; In re McDaniel, 293 F.3d 1379, 1384, 63 U.S.P.Q.2d 1462, 1465–66 (Fed. Cir. 2002).

The practical lesson is direct: if a dependent claim matters, argue it separately before the examiner and carry that separate argument into the appeal brief. A dependent claim that was never distinctly defended may not function as a meaningful appellate fallback. In a litigated reexamination, separately argued dependent claims may be the patent owner’s best insurance policy.

VI.       Amendments Are Available in Reexamination, But Often Not Practical in Litigation

In ordinary prosecution, amendment is a routine tool. The applicant may narrow a claim to avoid prior art, add limitations to align with a commercial embodiment, rewrite dependent claims in independent form, or pursue additional claims in a continuation. Amendment is often simply part of the path to allowance.

In ex parte reexamination, amendment is legally available but materially constrained. Section 305 permits the patent owner to propose amendments and new claims to distinguish the claimed invention from the cited prior art, but no proposed amended or new claim may enlarge the scope of a patent claim. 35 U.S.C. § 305; see also 37 C.F.R. § 1.552(b); MPEP § 2258.

When the patent is involved in litigation, however, the correct practical assumption is usually that amendment is not a normal option. It may be available as a last-resort validity salvage tool, but it is rarely litigation-neutral. A narrowing amendment can change the infringement analysis, undermine earlier claim-construction positions, create new noninfringement arguments, complicate expert reports, affect settlement leverage, and invite intervening-rights defenses. The litigation question is not merely whether an amended claim would be patentable. It is whether the amended claim would still be useful in the case.

The statutory intervening-rights issue is central. Section 307(b) provides that any proposed amended or new claim determined to be patentable and incorporated into a patent after reexamination has the same effect specified in 35 U.S.C. § 252 for reissued patents. 35 U.S.C. § 307(b). Section 252, in turn, preserves continuity only to the extent original and reissued claims are “substantially identical”; otherwise, it creates protections for persons who made, purchased, offered to sell, used, or imported accused articles, or made substantial preparations, before the reissue. 35 U.S.C. § 252.

The Federal Circuit has applied these principles in the reexamination context. In Bloom Engineering, the court explained that unless a claim granted or confirmed after reexamination is identical to an original claim, the patent cannot be enforced against infringing activity before issuance of the reexamination certificate; “identical” means without substantive change, not necessarily verbatim identity. Bloom Eng’g Co. v. N. Am. Mfg. Co., 129 F.3d 1247, 1250 (Fed. Cir. 1997).

That is why amendment can be so costly in litigated reexamination. A patent owner may emerge from the USPTO with a patentable amended claim but lose meaningful past damages for the claim as amended. The patent owner may also hand the accused infringer a new argument that the asserted claim scope has changed materially. In that sense, amendment can solve the PTO problem while creating a litigation problem.

The point should not be overstated. Some amendments may be unavoidable, and some amendments may preserve valuable prospective rights. A rewritten claim that merely restates an issued dependent claim in independent form may not necessarily change the scope of that dependent claim. See Bloom Eng’g, 129 F.3d at 1250. But as a rule of thumb, when active litigation is pending, every proposed amendment should be evaluated as both a USPTO filing and a litigation filing.

VII.   Existing Dependent Claims Are Often Better Than New Amendments

Because amendments can trigger intervening-rights and litigation-position problems, existing dependent claims often become the preferred fallback. If a dependent claim already recites the narrowing limitation needed to distinguish the cited art, the patent owner may be able to defend that issued claim without changing the claim text. That can be far more valuable than amending an independent claim to add the same limitation.

This is where prosecution strategy and litigation strategy converge. The reexamination response should identify which dependent claims preserve commercially meaningful infringement reads. It should then separately argue those claims on their own limitations, not merely as appendages to the independent claims. The purpose is not just to persuade the examiner. It is to preserve a clean record for appeal and enforcement.

For example, instead of writing, “Claims 2–10 are patentable for at least the reasons discussed with respect to claim 1,” the response should say something more concrete:

“Even if the Office maintains the rejection of claim 1, claim 4 is separately patentable because the applied references do not disclose or suggest [specific dependent limitation]. The Office Action identifies [reference passage] for the broader limitation of claim 1, but does not identify, and cannot identify, any teaching of [dependent limitation] arranged as required by claim 4.”

That kind of argument does three things. It gives the examiner a claim-specific reason to withdraw the rejection. It gives the Board a separately preserved issue on appeal. And it gives the litigation team a narrower issued claim that may survive without amendment.

VIII.                  Litigation Coordination Must Precede Any Narrowing Position

A reexamination response for a litigated patent should not be drafted in a prosecution silo. Positions taken before the Central Reexamination Unit (CRU) may affect infringement contentions, Markman positions, expert reports, damages theories, stay motions, injunction practice, settlement leverage, and appeal. The MPEP recognizes this overlap: ex parte reexamination requests are frequently filed when the patent is involved in concurrent litigation, and if a patent in reexamination is or becomes involved in litigation, the Director determines whether to suspend the reexamination. 37 C.F.R. § 1.565(b); MPEP § 2286.

The overlap is especially important for claim construction. MPEP § 2258 instructs examiners to acknowledge a federal court’s interpretation of a disputed claim term in related litigation and to assess whether that interpretation is consistent with the broadest reasonable construction. The MPEP also recognizes that written patent-owner statements filed in court or before the Office concerning claim scope may be considered in determining the meaning of a patent claim during reexamination. 35 U.S.C. § 301(a)(2); 37 C.F.R. § 1.552(d); MPEP § 2258.

Marine Polymer illustrates why coordination is essential. The patent owner had obtained a district-court construction of “biocompatible” requiring “low variability, high purity, and no detectable biological reactivity.” In reexamination, however, the examiner initially applied a broader construction, relying in part on dependent claims that permitted slight or mild reactivity. Marine Polymer responded by canceling those dependent claims and urging the examiner to adopt the district court’s narrower construction. After those cancellations, the examiner withdrew the rejections and confirmed the remaining claims. Marine Polymer Techs., Inc. v. HemCon, Inc., 672 F.3d 1350, 1356–58 (Fed. Cir. 2012) (en banc).

The Federal Circuit rejected HemCon’s statutory intervening-rights argument because the asserted claims themselves had not been amended and were not new. Under § 307(b), the majority treated that threshold issue as dispositive. Id. at 1362–64. But the court also recognized that arguments and concessions made during prosecution, including reexamination, can affect claim interpretation and effective claim scope. Id. at 1363–65. Judge Dyk’s dissent underscores the practical risk: although his view did not control, he would have treated Marine Polymer’s cancellations and narrower construction arguments as a substantive narrowing sufficient to support intervening rights. Id. at 1372–78 (Dyk, J., dissenting).

For that reason, “narrowing position” should be understood broadly. It includes not only formal claim amendments, but also canceling claims, adopting a narrower court construction, distinguishing prior art by characterizing “the invention,” disclaiming embodiments, or arguing that a claim term excludes subject matter relevant to infringement. Before taking any such position, reexamination counsel and litigation counsel should confirm whether the affected claims are asserted, whether the accused products still infringe, whether the position conflicts with Markman or expert positions, whether it affects damages or injunction theories, and whether existing dependent claims can be defended instead.

The practical rule is simple: in a litigated reexamination, every narrowing position should be treated as both a USPTO filing and a litigation filing. Marine Polymer limits statutory intervening rights to amended or new claims, but it does not make narrowing arguments litigation-neutral.

IX.       Appeals From Reexamination Are Not a Slow Reset

Appeal practice is another area where ordinary prosecution and reexamination look similar but function differently. In ordinary prosecution, appeal may be one path among several. The applicant may appeal, reopen prosecution through an RCE, file a continuation, or pursue a modified claim strategy.

In reexamination, appeal may be the principal path when amendment would damage the litigation. The patent owner may appeal an examiner’s rejection to the Board after final rejection, but a third-party requester may not appeal and may not participate in the patent owner’s appeal. 35 U.S.C. § 306; MPEP § 2273.

Because reexamination proceedings, “including any appeal to the Patent Trial and Appeal Board,” must be conducted with special dispatch, appeal from the CRU should not be treated as a slow opportunity to rebuild the case. 35 U.S.C. § 305; MPEP § 2261.

Appeal also reinforces the importance of dependent-claim preservation. The appeal brief must explain why the examiner erred as to each contested ground of rejection; arguments or authorities not included in the appeal brief generally will be refused consideration for that appeal. 37 C.F.R. § 41.37(c)(1)(iv). And, as noted above, grouped claims may stand or fall with a representative claim. Id.; MPEP § 1205.

A well-drafted reexamination appeal brief should therefore carry forward the structure created in the non-final response. It should separately identify independent-claim arguments, dependent-claim fallback arguments, claim-construction issues, evidentiary arguments, and any issues that must be preserved for further review. The appeal brief should refine the record, not create it for the first time.

X.          Conclusion

Responding to an Office Action in ordinary prosecution and responding to an Office Action in ex parte reexamination may involve similar tools, but the strategic posture is fundamentally different. Ordinary prosecution is about obtaining claims. Reexamination is about preserving issued rights.

That difference is most acute when the patent is in litigation. In ordinary prosecution, amendment is often a practical path to allowance. In litigated reexamination, amendment may preserve patentability while sacrificing infringement coverage, past damages, claim-construction positions, or settlement leverage. Because amended and new reexamination claims are tied to the intervening-rights framework of § 252, the patent owner must treat amendment as a litigation event, not merely a prosecution event. See 35 U.S.C. §§ 252, 307(b); MPEP § 2293; Bloom Eng’g, 129 F.3d at 1250.

The best reexamination responses therefore tend to be argument-first, amendment-averse, dependent-claim focused, and appeal-conscious. Counsel should make all available arguments in the non-final response, separately defend meaningful dependent claims, present evidence early, coordinate every narrowing position with the litigation team, and remember that appeals from CRU reexaminations are themselves handled with special dispatch. The response should not simply try to get past the examiner. It should preserve the patent, the appeal, and the case.