I'm currently building a commemorative paint F-16. This bird only carried a pair of AIM-120's on the wingtips. Should I fill in the holes for the under wing pylons or leave them open as mounting places? I'm not sure how the real plane looks without ordinance under the wings.

You should fill the holes ! The fixation for real life pylons is done differently... and I don't know how it's done ! Anyway, if you check pictures of ordnance free F16s, you won't be seeing any hole.

I may be mistaken but I'm not all together sure that the F-16 carried an AMRAAM missile on the tips? Certainly not the Block 10 aircraft anyway!
I thought that the wing tip pylon was reserved for AIM-9 sidewinders.

Later variants (And I do not know which block number) do carry AMRAAM's on the wing tip. I first noticed it on F-16s in Kosovo.

Well I can tell you for a fact that this block 30 carried them. The box art is an inflight shot of the plane carrying them. (I thought it unusual at first too) I personally think it looks better with the AIM-9's, but looks don't win dogfights.

Thanks penpen. That was my thinking, but all the pics I could find that showed underwing had weapons loaded on them.

Many airshow demo F-16s have all pylons removed, so I looked for reference pictures I may have taken that had the underside of their wings in it and I had one! There are tiny-tiny holes where the pylons mounted, practically invisible from more than several feet away, so you certainly want to fill the holes.