The right side bracket is also used as a muffler mount, so if that's to be retained, then the footpeg mounting boss will need to be cut off and smoothed, similar to what's described below. In this case, I'm using a high-mount aftermarket muffler so I could simply unbolt the right side assembly from the subframe.
The left side, however, also serves as the handhold for raising the bike on its center stand and locates the seat/helmet lock (above). To keep the functionality of the handle and lock, I bought a used bracket on eBay and cut off the lower portion, eliminating the footpeg but preserving the handle and lock. By sourcing a used bracket, I'm able to provide the next owner both original brackets in case he/she would like to revert to stock.
(Below) I then mark a cut line, and, using a larger cutoff tool, carefully make the cuts. Another 20 minutes of grinding, filing, sanding and polishing results in a smooth factory-like handle and lock. Shown here is a 4th-gen.
(Right) I've also trimmed the passenger pegs from a 2d-gen model. This was done to clean up the muffler mounting area. In the case of the 2d-gen, the steel bracket is welded in place so this modification is permanent, requiring a replacement of the entire subframe to revert to stock.