When are you taking the scales off the skin, before or after you glue the skins to the bow? Easier to get them off after. SOS is right. You can very lightly sand after you've put on a few coats of finish, but some texture will remain. I consider that a plus.
If your skins are thin, the underlying bow wood color can darken or lighten the skins very slightly. To darken, or even change the color of, the finished skin, it's also possible to stain or dye the inside of the skin before applying it to the bow.