For surface scratches you can get a Novus Acrylic cleaning kit from The Container Store. They are usually on one of the impulse shelves by the check out. This kit has three bottles of different type polishing liquids.
If you deep scratches, you can get an acrylic scratch repair kit at a good wood working shop. I got some from a wood working shop across 635 from the Town East Mall (It's in the little strip mall with Vitamin World I think). This kit contains various grit sand paper sheets.
Both take a lot of time and effort, but will polish out almost any scratch.
I have an 8' tank that one of the kids made a "mountain" looking scratch about 6' long when the little guy was helping me clean it with the magna float. Of course I had to drain the whole tank for that one.
Be gentle, patient, and persistent. Muscle and speed will only cause you to have to work harder to get a good polished finish.