I filled and repainted mine using Bondo spot putty, touch-up paint, sandpaper, and rubbing and polishing compounds. It wasn't perfect, but the patches were imperceptible unless you were really close and actually looking for them.
Since I didn't do a good enough job prepping the surface, within a year black circles started to appear as the raised plastic ridges around the holes started poking through.
I have the whole front bumper off as we speak, so while it's off I'm re-doing the license plate hole patches from scratch, using lessons learned from the first time.