Are you putting a full playfield mylar on the game? I didn't realize they made those for Sterns, so I'm actually thinking you are talking about the PF protectors that are real thin plastic. If it's that, then no need to worry about filling anything as it wont effect those. If it is actual mylar then you would be best to level it. Depending on if you are concerned about cosmetics or just leveling you could:
- Not concerned about cosmetics - Use some clear coat to gradually fill it in. You can get a kit from Stern or you could use something as simple as clear touch up (like car touch up paint) that can be bought at any auto parts store. This will fill it in but wont do anything for the appearance of the damage
- Concerned with cosmetics - match the color of the paint with touch up paint (art supply store could help here) and fill in the spots with that paint. One is in a spotted section so you could fill it in with the base color and use a toothpick to try and recreate the dots. Wont be perfect but would hide the damage a but.
After either of the above is done and dry you can then put mylar over it to seal it in.