I actually had to do this years ago. I bought a wet/dry kit from somewhere I don't recall, but as slief said you start with roughest grade and work in one direction to cover scratch. Move to next grade and work in opposite direction only. Next grade, opposite direction and so on until you get to the finest grade where it basically feels like you're rubbing wet paper over the acrylic. After that you shouldn't see the scratch from the front anymore nor should you see swirls. You may however see it from the rear side as looking through a side pane at the back of the front panel. Sometimes algae forms weird there too as its no longer perfectly flat anymore.
I did it while the reef was up and running, under water. The skimmer and overflow took out the fines, and I believe they're inert to the tank inhabitants anyway.
Good luck!