Remove all screw plugs from the wood boards with an electric drill.
Tap the tip of a chisel in between the wood boards on the floor. Then work the chisel underneath the wood board to create a gap large enough for the pry bar. The chisel will most likely cause slight damage to the side of the two boards it's in between, so work between two sacrificial boards. The sacrificial board should be in a corner, preferably under a piece of furniture so if you need to put it back down, it will not be visible.
Cut along the length of a sacrificial board with a circular saw to create an opening wide enough to fit the pry bar, if the chisel and hammer did not help. Avoid cutting a nasty gash into the board if you will reuse it; before laying the sacrificial board back down, fill the cut with wood filler.
Wedge the tongue side of the pry bar into the cut and pull the board up in the direction of the nail. Work from one side of the board to the other side, pulling it toward the nail each time.
Pull up the next wood board using the tongue of the pry bar once the first is free. Then repeat the process to pull up additional wood boards on the floor.
Remove any nails from salvaged pieces of wood and the floor with locking pliers.