Samster
Is the tank new or use? If it's a used tank, and the scratches are very bad, you probably want to get a professional and let him take out the scratches.
If the tank is new, and you're just worried about how to get rid of internal scratches, when you get them, you can use the kit that Warren mention above, I think that's the one you can use under water. You should also practice on the cover before you try it on the tank itself.
As for scratches, if you're careful they really shouldn't be a problem, and actually you'll probably hardly even notice them, specially on a large tank. You do want to make sure you keep up on cleaning and be very careful with the things you use to clean the front glass.