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Are you asking how to adjust the window, replace the felt, or remove the scratch? If the scratch is fine enough, you can get it out with #0000 steel wool. This has worked for me since the previous owner apparently rolled his windows up and down when he off-roaded my Vette in the coal mines. As far as adjusting, well, someone else will need to answer :D -Matt-
Scratches on the outside of the window come from 3 main sources: 1) those little black felt pads being worn out; 2) the outside seal (the rubber thing at the top of the door and at the base of the window). The metal backbone at the base of the seal rusts and scratches the window; 3) and the third and least likely is grit stuck in the outside rubber seal.
To avoid any more scratching, replace both the seal and the felt pads.
I have a bad scratch in my driver side window outside. It came from one of the rivets that hold the outside moulding to the door. Worked it self loose and before I noticed it scratched the window.