Egress window covers will keep water and debris out of the egress itself. They still allow for natural sunlight to enter the actual window, but keep pesky bugs, tree limbs, and yard clippings out of a hard to clean area. They also create an additional level of security by not allowing direct access to sunken windows. Scratches in these covers can be unsightly. Fortunately they can also be easy to repair.
Most egress window well covers are made of a heavy duty clear plastic. Scratches in plastic can be made less noticeable, but may not be able to be repaired all together. You can try to apply basic furniture polish and allow this to sit in place for 10 minutes or so. Wipe away the polish, leaving it on the scratch. The scratch should be much less noticeable. Another option is to use a CD repair kit and follow the instructions provided.
While it's more rare to see, some egress covers are made of a tempered glass material. Scratches on glass egress well covers can be fixed using household toothpaste. Be sure the toothpaste is an actual paste and not a gel. Cover the scratch with the toothpaste, and use a soft rag to gently buff over the scratch. This should make the scratch less visible.