Taking allowable subject matter during the appeal process

At any time during appeal, an Applicant with an indication of allowable subject matter can accept the allowable subject matter and back out of the appeal. To do this, the Applicant should file an Amendment under § 41.33 that rewrites the allowable dependent claims as independents, and cancels the existing independent claims. The Amendment should be filed as a separate paper, not as part of a Brief.
 
The Applicant in Ex parte Riley (PTAB 2014) went to appeal in 2012 with all claims rejected. In the Appeal Brief, the Applicant argued each of the three independent claims, as well as dependent claims 3, 4, 10, 15, 16-17, and 20. The Examiner found the argument for dependent claims 15 and 20 to be persuasive, and withdrew these rejections in the Answer. The Answer also stated that claims 15 and 20 would be allowable if rewritten into independent form. In response, the Applicant filed a Reply Brief that cancelled the independent claims and rewrote the indicated dependent claims into independent form.

The PTAB issued its decision more than two years later. The Board first noted that 37 C.F.R. § 41.41 doesn't allow amendments in a Reply Brief. The Board then treated the Reply Brief as "an indication that Appellants do not desire to present arguments as to the remaining rejections" and therefore "summarily sustained" the rejections of all claims except the allowable subject matter.

Instead of trying to amend claims in a Reply Brief, the Applicant should have skipped the Reply Brief and filed an Amendment under § 41.33.  As explained in MPEP 1206, amendments at this time (after the Appeal Brief and before jurisdiction has passed to the PTAB) are limited to: 

• (1) To cancel claims, where such cancellation does not affect the scope of any other pending claim in the proceeding, or
• (2) To rewrite dependent claims into independent form.

This procedure for taking allowable subject matter once an appeal is underway is unaffected by the appeal "forwarding fee" that became effective in March 2013.

In the Riley case, the Examiner's Answer had good news, in the form of allowable subject matter. But sometimes the news is not so good. Sometimes the Applicant reviews the Examiner's Answer and realizes that the arguments for the pending claims are not as strong as once believed. The best course of action may then be to pull the case from appeal and amend the claims. To do that, you'll need to file an RCE. As explained in MPEP 1215:

Prior to a decision by the Board, if an applicant wishes to withdraw an application from appeal and to reopen prosecution of the application, applicant can file a request for continued examination (RCE) under 37 CFR 1.114, accompanied by a submission (i.e., a reply responsive within the meaning of 37 CFR 1.111 to the last outstanding Office action) and the RCE fee set forth under 37 CFR 1.17(e).