MPEP § 2642 and § 2686.04 relate to the Office policy controlling the determination on a request for reexamination and the subsequent examination phase of the reexamination, where there has been a federal court decision on the merits as to the patent for which reexamination is requested.
Claims finally held invalid by a federal court, after all appeals, will be withdrawn from consideration and not reexamined during a reexamination proceeding. A rejection on the grounds of res judicata for such withdrawn claims will not be appropriate during reexamination. One of the essential elements of claim preclusion (res judicata) is the involvement of the same parties, or parties in privity with the original parties. The doctrine of res judicata based on a court holding in an infringement proceeding is not applicable in reexamination proceedings, because the Office was not a party to the litigation.
In In re Trans Texas Holdings Corp., 498 F.3d 1290, 83 USPQ2d 1835 (Fed. Cir. 2007), the court held that issue preclusion (collateral estoppel) could not be applied against the Office based on a district court holding in an infringement proceeding, because the Office was not a party to the earlier infringement proceeding and did not have “a full and fair opportunity” to litigate the issue; See also In re Construction Equipment Company, 665 F.3d 1254, 100 USPQ2d 1922 (Fed. Cir. 2011), in which the majority did not adopt the dissent view that reexamination was barred by claim preclusion (res judicata) or issue preclusion (collateral estoppel).