Thank you both. The scratches are not deep enough to feel. It's an area that's about an inch wide on the drivers door, where the felt was worn off the window guide, and it actually dulled the glass from rubbing there. If I can't polish it out I can live with it, but I would like to try to get it looking better.

 

whats the best way to remove the old weatherstriping thats stuck to the sides? and the glue?

 

If you're going to paint, then don't worry about the doors and just rip it off. Then use a wire brush and a scraper to get all the glue and old rubber off. Might even have to use a razor knife for some of it.
If you're not painting, then scrape it being careful not to scrape the painted surfaces. I found a thin little scraper at the hardware store that was only 3/4" wide, and I used that to get into the trunk groove to clean it out good.

 

well i'm taking off the trunk weather stripping but its stuck on the sides of the groove..would acetone work to remove the old glue?

well im not getting my car painted for awhile..was the thin little scraper like a putty knife?

 

Probably, but it might take off paint too! As long as it's almost all off, and glue residue that's left wont stop it from sealing. Doesn't need to look like new to get a good seal.

 

well it still has some of the old weatherstripping attached to the sides of the grooves after i pulled off most of it