Originally Posted by mARC

^ Quick and easy way would be to get some rubber bungs and touch-up paint.

Long term solution 'what we use to do', is make up metal pieces and weld them in 'dependent on hole size', then prepare for painting as required.

Be careful when getting quotes as some people are known to just put filler from the roof lining to the holes. This is a cheap and dodgy fix as you'll encounter sink back and the possibility of the repairs vibrating loose.