I had to do some compounding work on a few sports on my car.  How do you remove the marks left by the compound? 

I'm pretty sure rubbing compound takes off the clear coat. Is that what you are referring to or light scratches left in the paint?

I've never used rubbing compound, so I don't know an answer.
Though, I wonder why it was used on a fairly new vehicle.

From what I remember, rubbing compound is a fine liquid "sand paper" that removes the upper surface of paint and is used to remove oxidation and the like.  As such, it removes paint.  A "repair" would involve smoothing it out.  The best way depends on the depth of the surface and the amount of surface material/paint/clearcoat removed by the compound.  a good waxing or whatever the recommended finishing for the rubbing compound should remove minor scratches.  If greater, have a detailer (more experience, tools, and supplies) look at it and tell him/her exactly what you need.
Again, I am using reasonable speculation and educated guessing.  A detailing expert would be better.  I have "issues" washing my car(s) more than once a month, averaging once every 1,000-2,000 miles . . .

Before you repaint, have a GOOD professional detailer look at it.

Otherwise . . .
This is a GOLDEN opportunity for a UNIQUE color box!
You could also make a cool complex paint scheme . . .

It sounds as if the "clear bra" from 3M is actually the same or similar thing they use to make auto wraps.  The info about the wraps actuallys says that it protects the car's finish. 

One might find a sign shop locally with the experience to apply the vinyl  on all the angles - it would just be clear & unprinted.  And it's supposed to be easily removed by pulling diagonally at a very sharp angle.