This is how I removed an annoying ridge on my GTS's seat, but the procedure is basically the same for any modification.
First of all the seat is removed by unscrewing the 2 10mm bolts in front by the hinge. The seat is then placed upside-down on a towel or other soft surface and the staples holding the cover on are removed by prising them up with a thin, flat-bladed screwdriver, then pulling them out with a pair of needle-nosed pliers. On the GTS there are 2 plastic pieces on either side that take the place of the seat strap mounting points of the GT seat. These are removed with a Phillips screwdriver. The cover can now be carefully removed exposing the foam padding. With the seat right-side up, using a Sharpie marker, draw a centerline and other reference lines to ensure symmetry when cutting the foam.
Now for the fun part, shaping the foam! I find that an electric carving knife does a great job of slicing through the foam, although I have had reasonable success using a bread knife or hacksaw blade. Carefully slice away the foam, keeping both sides symmetrical, until nearing the desired shape, then use a Stanley Surform plane, a rasp or rough file, followed by rough sandpaper to smooth out the foam. The foam lends itself surprisingly well to carving and small imperfections are usually hidden by the cover, so don't be nervous about this! At this point it is advisable to place the seat back on the bike and sit on it to test whether you've achieved the desired effect. Better now than after everything is buttoned up!
Once satisfied, the cover can be replaced and restapled. Be sure that the cover is on straight and aligned properly. This can take some pulling and pushing. Turn the seat upsidedown and starting from the back, using 3/16" staples in a stapler, insert a staple in the center. (See photo below for correct position and sequence). Pull the cover towards the front and rolling the material over the edge, insert another staple. Having an assistant to help hold the material, while you use the stapler will make this go a lot easier. Proceed placing staples on either side while ensuring that the cover remains correctly lined up and tight. Once anchored down by the front, back and side staples, the remaining spaces can be filled in. This procedure is not as tricky as it sounds, but it does require strong fingers and hands. An electric or air-operated stapler would make the task a lot easier.
All that's left is to bolt the seat back on the scooter and go riding. Your butt will thank you for it!
Carving foam with electric carving knife
Final smoothing out with sandpaper