How should I fill 1/8" nail holes in a hardwood floor?
Most engineered and laminate floor installations come with a repair kit such as this. They can also be found in home centers.



It usually consists of wax crayons color matched to the floor to rub into small nailholes or other imperfections.  These are rubbed over the hole to fill it, scaped flush and then buffed slightly with a dry cloth.

Because they are wax, they cannot be coated with a finish, but for small holes this generally is not an issue

A hadware store can provide the wax crayon fillers such as these:



Pick a few colors.  They can be blended and will come in handy later on.

The kits also usually contain a small bottle of a polyurethane type finish matched in sheen to the floor for scratches.  In theory, you could fill, stain and then seal small nail holes with this finish, but usually not done.

Finding a small bottle of matching scratch filler will be tougher than wax fillers and the process more compicated.