I would fill the holes in with caulk or maybe even RV type so it's weather proof and slap a good quality sticker/tape/adhesive as close to the color as you can get it and no one will notice it except you.
You can fill it up with bondo or similar product, clean it up and repaint although I wouldn't do that. You can slap a K&N or similar sticker on it. Not only it'll cover the holes but will add like 7 ponies