1. Filling in holes within a scan:
Click:
Scan Repair tools
Detect border: The hole you want to fill should be outlined in green. If it is not, click "cycle borders" until highlighted.
If you have more than one hole, when highlighted green click "add to border group", then "cycle borders" until you outline the second hole.
Once all your borders are highlighted green, you can click "Repair borders" to close.
2. Small holes in the scan:
Many small holes in scans can be fixed with this tool found within "repair scan tools".
If the holes are large, I recommend creating a bridge within the hole and then repair those individual holes.