Patrick… This is what I did on my first tric build. I plan on doing this for teh current build as well.
Using the plans by trekme ( TOS Hero tricorder - a how-to wiki ) I taped off all of the areas to keep and then sanded down carefully, a little at a time, leaving some spare material. Then test fit, sand a little more, test fit, and so on. Once you have the height you like use a file to trim the angles.