[firetruck41]

They make wood filler for exactly that application, should be able to get from a hardwood supplier, it comes in different tones, and you just quickly fill all surface imperfections using a putty knife, before you sand/finish (you do the same thing with holes from the nails in the face nailed boards on the edges of the room). The imperfections will nearly disappear, by the time you have sanded and finished the floor. If you have a bunch of actual holes, you may need to do something different.