I just sand them a little bit and then fill them with two part Epoxy.
While it is still liquid, I tape a piece of clear plastic film, (like overhead projector or loose leaf binder page protector) over it. The next day take the tape and plastic film off. (it comes right off), and usually the repair is as smooth as glass and only need a bit of sanding.
If the holes are not in a flat surface, disregard taping anything down on it, and you'll have to sand after the epoxy hardens.
If the hole is deep it might take several fillings.
For larger holes, I use epoxy wetted out fiberglass and still use the method described above.
Hardshell Kayak Sail Rigs