Carefully dig them out if you can. Otherwise, not much you can reasonably do...short of pulling it all up and starting from scratch.

If you can get them extracted, then you can insert a hardened spiral flooring nail in the hole and more easily countersink those. Spiral flooring nails have smaller heads and some have dimpled heads which make countersinking a breeze.

For extraction...go to a store that has a good selection of molding nail pullers, pry bars and such. You want a tool that will allow you to get underneath the nail head, so you can ease the nails out. You want something that looks like this: http://www.kentique.com/wp-content/uploads/2010/01/Pry-Bar.jpg Copy the link to your browser or click on the URL below.

Place a thin piece of metal, or other thin hard malleable material under the part of the tool that contacts the wood as you use the tool as a lever to pull the nails out. That will help reduce denting of the wood as you extract the nails. If some nail heads break off, don't worry; simply countersink those with a nail punch of a suitable diameter.

Here is a link that might be useful:

Roofing nail heads are closer to 1/2 inch diameter.

Sounds more like common nails.

They will be very difficult to sink in hardwood floors.

It may be less damaging to remove them and fill the holes.

If you must replace them after puling them, use finish nails.

Use a 1/4 punch instead of a nail set.
And get a heavy hammer.
They will go in and you only need to get below the surface for filler.

Thanks for all the input. Plan to dig out the nails that are high enough to do so. And, thanks brickeyee - they ARE regular nails, not roofing nails
Thanks Zagut - I wonder if there is a pneumatic type device that I can rent (or buy) to make it go easier?

Buy one of the longer pullers shown below. I have a cast iron model made before I was born(and I am 66) that still works perfect).

It does make two small gouges on either side of the nail head and you will need to put a putty knife under the fulcrum(the part that rests on the floor to pull out the nail) to prevent dents, but the damage done is way less than any other puller.

Here is a link that might be useful: Nail puller

The nail puller will make large gouges on each side of the nail head when it is hammered in to get a grip.

A drilling hammer (small hand sledge in the 2-4 pound size) and a metal punch that is the same size or barely larger than the nail head will get them in most likely on all nut the hardest of woods.

If you want it to look nice, it might be worth trying to center punch each nail head then drill the head off.

It is one of those things that the less work to sink them, the more work may be required to repair the surface.

To a certain extent the floor might be considered so damaged that it is only worth tearing it up and installing a new floor.

And I love old floors.

You might try a pneumatic palm nailer. (its a handy tool to have in the box in any event)

Pulling them out and plugging the holes might make for a neater job. Lots of good suggestions on pullers above.

You could use a screw extractor or very small hole saw to cut out a ~3/4" plug around the nail to allow you to get hold of it to pull it out, then plug with grain-matched plugs. This is sometimes done to hide screws with wide plank flooring that is screwed down. It's sort of a rustic look.

Here is a link that might be useful: example palm nailer at Amazon

Thanks for the suggestions, and yes, brickeyee, I love old floors..Last weekend, I went to a Lumber liquidators and came home with boxes of new laminate flooring.. My heart sank when I thought about covering my (beautiful) wood floors and couldnt bring myself to do it... So, will try these ideas. I am still thinking to rent out a pneumatic air hammer and use a punch bit to push in the nails, if possible. Fingers crossed...

The nail remover I linked to makes smaller gouges than the size of the nail head.

It has a built in slide hammer---does not need a hand held hammer.

A pneumatic hammer/bit will hit the nail head once and the floor around the nail head six times before you can release the trigger---making more holes to deal with.

My advice is based on actual experience---with the slide hammer puller, cats paw pullers, various other design nail pullers, and pneumatic hammers.

The slide hammer puller is by far the least damaging type to use.

Redundant post deleted.

This post was edited by handymac on Wed, Jan 23, 13 at 22:47

"The nail remover I linked to makes smaller gouges than the size of the nail head. "

A slide type nail puller makes a gouge on each side of the nail head aroun 1/4 in ch wide to get down below the head to pull the nail out.

They are sort of rough and tough tools.
Mine is from before 1900 (and still going strong).

They are far more intended for tearing apart packing crates than working on anything that has an appearance factor like a floor.

I think any puller even with a plate is going to cause gouges you won't want. Once you pull the nail you could drill a larger hole then plug it.
A pneumatic air hammer will be hard to control and you might end up with that woodpecker look. It would be nice to have a tool for everything but sometimes the old fashion way is the one that works.
Pulling and pluging will look the best but pulling old nails could be just as much work as setting them.
It all depends how much work and money you want to put into it. Set and fill is your least expencive option but only you can decide what's acceptable to you as the finished product.

Good luck.

Hi,
Since this has not yet been suggested, here goes.
Driving a headed nail into hardwood risks splitting the wood, most especially near the ends. Hard wood is hard, and does not take well to countersinking large heads.
I offer this alternative to removal: if you took a drill bit and a center punch, you could drill the heads off and then sink the nail as easily as if it were a finish nail, and leave just a small hole. Most labor-intensive, but least damage-causing. Perhaps you would still have the shadow of the nail head on the wood.
Casey