you cant "remove" a scratch as a scratch its self means a lack of matereal.
what you can do however, is fill in the scratch. i do not know of any aquarium safe scratch fillers though. all of the ones i know of for automotive applications would be lethal for fish. and failing that, i do not know of any scratch fillers which can work underwater.
i would suggest to be safe, ignore the scratch or replace the piece of glass. most glass stores can cut you an exact replacement piece for pretty cheap. aquarium glass as far as i know does not have any special properties in it so it should be pretty cheap. and aquarium silicone is cheap as well.