Vacuum the area around the holes and in the holes to remove any loose dirt that might muddle up your repair putty. Use a shop vacuum with a filter to clean up dusty areas without blowing dust over the room.
Sand over the surface of the wood floor around the holes. If you are working on a whole room, use a room-sized sander, or if you are working on just a small area, use a hand-held sander. Vacuum again after the sanding process to remove the sanding dust.
Wipe the area with a tack cloth to remove any fine dust clinging to the surface. Clean the surface of the sanded wood with a clean rag dipped in denatured alcohol. Turn the rag often to keep using a clean surface on the floor.
Push wood putty that matches the color of the wood floor into the nail holes using a small putty knife. Work the putty into each hole so that there are no gaps. Allow the putty to dry the putty for the amount of time recommended by the manufacturer. Sand the putty lightly in the direction of the grain and wipe clean with the tack cloth.
Stain and finish with the rest of the floor.