Live in an old house where the nails rise up from time to time from out of
the pine floor.

Years ago I went around pulling some of them up and replacing them with long
screws. (The Phillip heads don't look nearly as nice as the old rustic
nails... I should cover the screws with some wood-filler type stuff.

The tops of the nails are rectangular. The problem is that some of them
don't rise up very much and it's difficult to remove them without
occasionally damaging the surrounding wood.

I used a screwdriver type tool that has a curved v-shaped claw to it.
Crowbars and hammer claws are too thick to fit beneath the nails.
Sometimes, I couldn't grab the nail and damaged the wood slightly to get at
it. Anyone recommend a less damaging method? And, any cosmetic substitute
to using long screws other than covering them up?