the obvious is not to put them there.
well covering that, are they inside or out of the tank?
Inside, you cant do much
Outside isn't that hard if thery are not that deep. How thick is the acrylic?
What you do is get some fine (1200-1500 grit for light scratches, maybee 800 and move up for deep scratches)wet sand paper on a sanding block and sand it in a circular motion (with water and a little soap to lube).
After the scratch is flat with the sanding scratches, now you flame polish it.
Get a small propane torch (benzomatic style) and lightly go over the sanded area. If you get to close, it will bubble, if you too far it won't do anything (better to far to start with) about 6 in is good. YOU MUST KEEP THE TORCH MOVING AROUND. DO NOT LEAVE THAT KIND OF HEAT IN ! SPOT OR IT WILL COOK.
This works, but takes some practice. Buy a 5 or 10 ga acrylic tank to practice on first. $15 worth of practice WILL save you hundreds in show tank.
Have fun.