First off, do not use sand paper. The sandpaper grit will wear off over use (which is it's function) and possibly remain in the dough. You don't want anyone eating sand paper grit, and I'm not even sure what it would do. It might even be a hospital-level problem if the grit gets embedded in any digestive tract tissues and causes inflammation. Ugg. Please don't.
If you have a mandolin slicer and the cookies are soft enough, you could set it up on a very thin setting and slide the cookies across the bottom, shaving off a tiny bit.
I like the sandwich idea above.