If they are surface scratches then I believe they can be removed with a rubbing compound called Jewllers rouge. This is a fine white powder that you should be able to get from your local glass supplier. You mix it with a little water until it is like a paste then you put it on the glass where the scratch is and you rub it in but doing it in a circular motion and you continue this over an area bigger than the scratch until the scratch disapears. A word of caution!!! do not use your finger to rub it in as the rouge will remove your skin as well as the scratch, use a stick of some sort to do this part, to find out if the scratch can be got rid of. Use the end of your finger nail on your thumb and rub it over the scratch if your nail catches in the scratch then it is too deep to remove using the rouge. If it is deep and you use the rouge to try to remove it, it will leave a concave hollow on the glass and give you a rainbow effect and this will be more readilly seen than the original scratch.
That's the theory anyway.