Hi-
Do you notice these smudge marks with the iMac off as well? If so, it is probably just some dirt or a fingerprint behind the glass on the front panel.
Yes, Apple or any authorized repair center can do this. 5 minutes tops. You could probably do it yourself (if out of warranty, which you are not) with a pair of suction cups to lift off the glass.
Again- you are under warranty, so I most certainly wouldn't do that.
Some users post being able to get a replacement iMac while their defective unit is in the shop, but those individuals have either had a history of having problems with their order, or were especially forceful in manner.
Don't count on being able to get one.