Looks like some type of epoxy or some other type of substance has eaten its way through the clear coat and bonded to the paint, I have tried to use an on the shelf cleaner to remove it and it did not even make a difference, there is just about an inch of spots total area affected. Any ideas on what I should do? Take it into a professional detail shop or auto body shop?

 

If you can feel it on the surface then detailers clay might take it out.

 

This won't work if it's epoxy, but mechanic's waterless hand cleaner is really good at softening and removing lots of things. (No pumice, please.) I like the orange based ones because some of the others smell pretty foul.) Just glop some of the stuff on, let it sit awhile, then wipe or rinse it off. You don't have much to lose by trying.