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General rule is if the glass scratch catches your finger nail, then forget it. If not that bad you can try polishing it out with a drill motor mounted glass jewler's rouge wheel kit from places like Griot's or J.C. Whitney. Expect some patience and elbow grease to be involved in this though.
My removable rear window has some scratch marks where it was hit when the rear deck was sanded during paint prep....why did they just not remove it !!!!
This all happened prior to me getting it but I spent a bit of time looking into how to fix it and I agree if you can feel them then the chances are you wont fully get rid of them.
However you can certainly make it look better...
I have used burnishing cream and cloth buff and it took almost all the fog out of the glass around the scratches.
Then got a 2" felt bob and polishing powder (to be mixed to a paste) on ebay.
Have not tried it yet but just the initial buffing with compound made a big improvement.
I've used the Eastwood product. Yes, this is very time consuming. I spent 2 solid hours polishing the drivers door glass (out of the car). It certainly helped the overall appearance of the glass but didn't get all of the scratches out. Be prepared for a mess as the polishing compound gets splattered over everything.
I bought a Lake Country Pro Glass Polishing Kit a while back to try on my other cars. I heard it was one of the better kits to try polishing glass with.
On a different note if you ever have to remove water spots etched into glass. There is this stuff call Spot-x that works awesome.