I have a new pine floor finished with 2 coats poly. What should I use to fill in some countersunk nail holes before 3rd coat of poly?

I have a new pine floor with 2 coats oil based poly (no stain). I want to fill in numerous countersunk nail holes that were left unfilled. I will be putting down a 3rd coat of poly after that. Would Elmers Wood Filler work, or is there a better solution? I want to make sure whatever I use will stay put. Thanks!