The only real method of removal is to sand floors down putty and apply new stain on the entire floor that is dark enough to hide these marks.
How to fix nail holes in wood floor.
Hold a scraper at a 45 degree angle with the blade flat on the wood.
Use a putty knife to put the putty into the holes in small quantities and press it down so it fills the holes completely.
Begin by taping off the area around the holes voids or knots.
Don t use just any glue though or it may discolor the sawdust.
As the stain goes beyond the hole into the wood and all that the putties and wax for that matter will fill the holes and not cover the stain itself.
You re still going to see a little bit of them but they will not be obvious.
Typically your fingers will suffice but use a putty knife if necessary.
Avoid pva or carpenter s glue.
Wipe off excess putty with a damp rag.
Choose a wood filler that matches the color of your hardwood floor.
Here are several different ways to fill holes in a piece of wood.
Sand it again and you ll just about cover them.
Pull a dab of putty from the container and press it into the nail holes.
The most reliable way to match the color of a species of wood to fill holes in a wood floor is to mix sawdust from that wood species with glue.
No matter what type of sawdust you mix the final color will be a dull yellow or even gray.
Apply a bit of extra putty over the hole so you have a small mound.
Use a cloth that has been lightly dampened with water to clean any excess filler from around the nail hole.
Knead a small amount of stainable latex wood filler like this one from minwax before pressing some of the product into each nail hole in turn using a putty knife or a three inch trowel.
You sand the wood floors you ll get rid of most of that black stain that s showing around the top of the hole.
Press the edges of the painter s tape down to seal it against the wood.