I got my 100G tank for free but it was scratched to hell. I took these steps and managed to get a LOT of very deep scratches out and it came out looking new.
First clean thoroughly, scrape off any algae, etc with a plastic scraper
Get 3M Wet/Dry Sand Paper in the following levels of grit (your lowest level is dependent on how bad your scratches are):
400-800
1000
2000
3000
Fill a pump up sprayer with water and keep the tank surface wet at all times while sanding. Not so wet that the paper just slides around but wet.
Start with the lowest grit paper and sand up and down - once all of the deep scratches are gone move on to the next grit - this time sanding left to right - now the goal is to remove the scratches created by the previous piece of sand paper. Then move on to the next grit sanding up and down again and so on. Each time you do this you are trying to remove scratches created by the previous grit until you get to the super fine stuff at which point you should be able to buff it out.
Its freakin hard work but pays off when you finally get to fill it up