Black dots on wooden stair treads, can't sand them away
A good filler will work for the nail holes but probably won't help with the black spots because there's not enough depth for the filler to take hold. Be sure to get a filler that will take stain as many don't. These stairs were probably meant to be carpeted from the start so quality lumber wasn't used. Your best bet would be to buy/rent a belt sander and sand the hell out of them. Even then, you probably won't get all the black dots out of the stairs. Then finish them as planned.