Remove a small amount of wood putty from its container with the blade of a metal putty knife. Mix the putty thoroughly on the lid of the putty can or a piece of cardboard.
Drag the blade of the putty knife over the mixed putty. Pull the wood putty loaded blade over a nail hole while holding the knife at a 45-degree angle to the surface of the door.
Allow the wood putty to dry for 5 to 6 hours.
Sand the dried wood putty by moving a piece of 180-grit sandpaper with the wood grain of the door. Continue sanding until the wood putty blends seamlessly with the area surrounding the nail hole.
Wipe the sanding dust from the door with a rag. Repeat the process on all nail holes in the door.