I've used a cat's paw pry bar and gently tapped the nails out...
And when that didn't work, I used a drill to remove some of the wood around the nail, then used the cat's paw again.
Recycled timbers are probably always going to show some scars...
Do you have a metal detector?
Make sure to run it over the timbers after you're done, just in case...! It sure sucks to hit a nail with a tool.