Removing scratches is difficult. It involves a buffing process and most times without the right skill, right tools and specialty pastes you will do more damage than good by creating cloudy areas. It is extremely hard to buff glass totally clear.
Sorry, I wish the news was better. I own a window company and I'll generally replace glass before I'll buff it because 9 times out of 10 I'll end up replacing it anyway..
If you do try, don't just take advice from an aquarium site, go and ask questions where they do this sort of thing. There's a forum for everything nowadays.