You are going to have to cut it flush. If you try and leave an overhang the material will flex and will bunch up right where you go to fold it over. I use to work in a sign shop and have flush cut polycarbonate about a zillion times and the secret is to get a brand new big razor blade, and run it perfectly strait with the edge of your piece. Don't try and use a small exacto (smaller blade means more of a margin for error). Take the material in several passes, don't necessarily try to remove everything all at once. Start by chopping off the bigger areas, and leave just a small enough amount so that you can pull the material away as you are cutting it. If your blade starts to get some residue all over it, just wipe it off. The cleaner you keep your blade the less likely it is to bind up and cause you to make a mistake.
Go slow and take your time. It is a bit tedious, but extremely rewarding once you finish.