The USPTO, in a release from October 5th, has issued a "Notice of Clarification of Office Policy To Exercise Discretion in Reexamining Fewer Than All the Patent Claims." The USPTO acknowledged that the 8th Edition Revision 4 MPEP included language within MPEP § 2258(IV)(B), regarding ex parte reexaminations, and MPEP § 2658(IV)(B), regarding inter partes reexaminations, resulted in "a public perception that the Office is required to examine all claims of a patent, once ... reexamination ... is requested for at least one claim of a patent and the Office then determines that a SNQ [substantial new question of patentability] is raised for at least one claim." The USPTO then notes that this issue was clarified in Sony Computer Entertainment America Inc., et al. v. Jon W. Dudas, Civil Action No. 1:05CV1447 (E.D.Va May 22, 2006), Slip Copy, 2006 WL 1472462, where the court noted that the 35 U.S.C. §§ 311-313 were clear that reexaminations would be performed on the claims requested to be reexamined by the requester, and that the USPTO was not required to reexamine any claim not specifically requested. This has been memorialized in the 8th Edition Revision 5 MPEP at § 2258(IV)(B), regarding ex parte reexaminations, which now states in relevant part that "The Office's determination in both the order for reexamination and the examination stage of the reexamination will generally be limited solely to a review of the "live" claims (i.e., existing claims not held invalid by a final decision, after all appeals) for which reexamination has been requested. If the requester was interested in having all of the claims reexamined, requester had the opportunity to include them in its request for reexamination. However, if the requester chose not to do so, those claim(s) for which reexamination was not requested will generally not be reexamined by the Office." The language stating in part that "each claim of the patent will be reexamined" has been removed from the MPEP to support this clarification. A similar change was made for inter partes reexaminations in the 8th Edition Revision 5 MPEP at § 2658(IV)(B).

USPTO Notice of Clarification: LINK
MPEP § 2258 (Revision 4): LINK
MPEP § 2258 (Revision 5) - within Chapter 2200: LINK
MPEP § 2658 (Revision 4): LINK
MPEP § 2658 (Revision 5) - within Chapter 2600: LINK