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When you're filling nail holes in unfinished wood, use a color-matched wood putty. Apply it to the wood with a putty knife, let it dry and then, sand it smooth.
For finished wood, you can't use cellulose putty because the necessary sanding would scratch the surface. Instead, use a color-matched wax pencil. Just rub the pencil over the nail hole and rub off the excess with your finger or a cloth.