I used thicker (1/4") plexi on my panel, clamped it down to the workbench and cut with a jigsaw. Medium speed for straight lines, low speed for corners. If the plexi is vibrating, sandwhich it between another piece of wood moved as close as possible to edge you're cutting. My saw let me get about 1.25" from the cut, enabling me to cut the corners and stuff without the plexi flapping.
After I was done, I hit the edges with a random orbital sander with 220 grit to get them nice and even/flat.