If your upper is brand new, you might work with your supplier to exchange it for one that might fit your Oly lower without modification. Sometimes "bad" manufacturing tolerances can work in your favor to get properly mating receivers.
If you're stuck with the parts you've got, then first determine why the upper and lower do not fit properly. Examine everything carefully as you close the upper into the lower. Where is the interference?? Is it upper takedown lug-to-lower walls? Is the lug too wide? Does the radius between the top edge of the lower up into the extension tube ring not match the upper? How is the hole spacing for the pivot pin and takedown pin? etc. etc.
Once you figure out what's not matching, you need to decide which parts you want to remove material from to achieve an acceptable fit. IMHO NEVER, NEVER remove material from a good lower receiver. In most cases milling, grinding, filing, reaming the upper to fit a lower will be invisible once the weapon is closed.
Once you get the fit you want, you can do nothing to the areas where you exposed the bare aluminum, get the parts re-anodized to cover your machine work, use one of the many gun coating finishes available, get a professional gun refinisher like Arizona Response Systems to refinish your receivers, or use that Birchwood-Casey Aluminum Black junk to darken the exposed aluminum.
Many times the failure of upper and lowers to fit properly is just a minor pin-to-pin spacing problem that can be easily corrected by using a very fine 1/4" diameter round file to CAREFULLY elongated the hole{s} on the upper receiver lugs. If you're REALLY SLOW and CAREFUL remove material the fit will be perfect and totally invisible.
Good Luck!