I recently got the Deluxe Earth Prime, and find that he's a really nice figure, much better then the Deluxe Megatron.

My only problem with him, is that his "battle damage" is really distracting. So I was wondering what would be a good way to remove it, and if it cane me removed without removing some of the other paint its ontop of.

Depending if you plan to 'repaint' the area, I've used a q-tip dipped in nail polish remover for spots.
This only works if:
You choose the non-acetone stuff—it's kinder to the plastic,
and your planning to repaint the area, as depending on the plastic, polish remover will sometimes 'dull' the plastic areas it touches.