Dear Donna
If you find that he used large headed standard nails, instead of finishing nails, don't try to set these nails below the surface of the wood, it will crack the hardwood. So instead go to www.leevalley.com and check out the restorer's cat's paw. I use the 12" model to remove the most stubborn nails from the surface of the wood with minimal damage. You just hammer the paw under the and gently pry up and out.
All that said, once you have removed all the nails, you may find that some of the boards are damaged beyond repair, go to the repair article I wrote available in the search box at the top of this web page. You should be able to do minor repairs yourself. And the holes the nails left should be filled with a colored latex filler, that will match the final color of the wood (if you intend to refinish it). If you don't want to refinish the wood now you can still use this filler, but you must be sure to wipe off all of the excess before it dries.
If the floor squeaks, there is a cure for this, but this is another question for another time.
Oh, and if re-sanding of the floor sounds too daunting you can try chemically stripping it instead. But you should also read the second part of the floor maintenance article, to see if you can save the old floor finish.
