If you still have some boards from when you laid the floor originally you can chissel out the scratched boards and replace them. You could also get some boards from a closet if you don't have any left.
If the scratches are not too bad, you can get a marker or puddy from the Minwax section of the matching color, and fill in the scratches. This will improve the look, but not like replacing the boards.
Replacing the boads will most likely require some sanding and restaining.