Hey man!
Its caused by the a few sponges, which is suppost to allow the window to slide up and down smoothly but as time goes the sponges turn hard and become hard dried up brisle brushes which leads to scratching.
I have not removed my window before but I have had to change my electric window mechanisim which requires fiddling around with the window.
Remove the iner door panel and you will see the window mechanisim, the one that allows the window to go up and down lead by metal wire.
There is an attachment or hinge and the window is bolted to that.
Un bolt it and slide the window out.
You could take it to your mechanic or take it to O'Briens windscreens and they could replace the window for you.