First off... results acceptable on a shower door may not meet the standards for a 40 gallon acrylic fish tank. It's a tedious process and not always completely successful.
I've used a product from an acrylic tank manufacturer previously that met my requirements most of the time, miracle mesh or something like that. It's also possible to use liquid products. Here in Houston the Container Store carries a series of bottles, coarse, medium and fine that when used properly would likely "erase" a mild scratch.
Obviously, you can't just use an orbital sander with a polishing pad. Don't laugh, some have tried it only to find circular scratches embedded in the surface obscuring the initial target of the process rather than removing it.
Whatever product you finally choose to use I'd change directions each time you change the compound or material. Carefully trying to remove the edges of the scratch leaving only the depression of the original scratch.
Good luck. Dan
