How do you remove Minwax stainable wood filler?
There is really only one way to rid yourselves of the "white" fill spots. You will need to carefully dig out a small amount of the filler so only dark wood is showing around the edges. You don't need to remove all the filler from the original hole. Buy a pre-colored filler crayon, Minwax and others make them. Match the color of the filler stick to your floor color. Sand a small area around your repair with fine sandpaper, an inch or two is plenty.  Fill the indent with the matching colored filler, smooth it well and put a couple of coats of urethane over the repair, feathering the urethane into the existing urethane finish. A foam brush would be good for this purpose.  Good luck.