How should I fill the holes in my floor to prevent mice from getting in?
Expanding foam can get messy but it may be your best bet, if you can keep it in place and they do not chew through it.

You may want to  either incorporate a heavy gauge metal mesh wire, neatly cut around or into the place the mice go through. You might could even "bed" the wire mesh in the foam as it is expanding to lock in place that way. Doing this will make a potentially messy task and make it even messier.

This will not look nice in any sense of the word on the larger holes but it will certainly slow them down for a while. Otherwise a cat, as mentioned in the comments section, will also take care of the problem.

Thin sheet metal screwed in place will work as well without the foam too. You could try nailing it down, but in the cabinet it will bounce a bunch, screws are better here.