When I have used Plexi before, I would trim it with a router round-over bit and then take a propane torch w/ flame spreader and put the least amount of heat to it. (A heat gun might be better, but I have never used one.) It would smooth out the cut marks left by the router bit. Don't heat it too much or bubbles and distortion start.
I suggest some practice on some scrap first to get the 'feel' of it!
