I have a scratch that is just on the clear coat, what is the best compound to fill it in?

 

If you can feel it with your fingernail, there isn't too much you can do about it - but you can minimize it with something like Meguiars ScratchX 2.0.

Got a pic?

 

Keep in mind that many products such as Scratch X and Ultimate Compound don't fill in scratches, they remove a small layer of the clear coat in order to remove the scratch. There are also products such as NXT 2.0 that are polishes and contain fillers to mask scratches.