You can sand clear parts, just sand it using successively higher grits, to remove as much of the rough sanding spots as possible. When you are close to done, the clear piece will look cloudy like the following:


At this point, either spray a clear gloss, or dip the part in some clear gloss. Future floor polish works as an acrylic based clear gloss. I used Mr Super Clear Gloss which is a lacquer based product and airbrushing it onto the part and this will fill in the small scratches leftover by the high grit sanding, and the clear parts will go from cloudly to perfectly clear. keeping in mind that you sanded with successively higher grits of sand papers



Long post short, you can sand clear parts, just clear coat it when you're done sanding.