I use a couple of different ways to cut them, but still get burrs and such where the cut was. I touch up that spot with a needle file.
BTW, I have one of those MM kits too. I have used it for a couple of scratch models, but it sure is a lot of work. I also have a set of toner transfer paper that is supposed to make PE parts, but the quality is nowhere near what you get with the actual photo process like the MM kit. Toner transfer PE okay for larger parts, photo process seems to be only way for really small parts, though.