My 3 year old son has ugly marks on his knees from constant falling. What can I do to remove the scars?

Nothing. Scars are the result of healing.They are made worse by being stretched over a joint.
Nothing, really. Try to limit new scars, because those there already are permanent. As he grows these will stretch and fade, but will always be there to some degree. There is nothing that can remove or eliminate them, but see a plastic surgeon for advice as to how to make them better if you wish. But this is pretty normal, and he's probably not going to be a model, so don't make the "cure" worse than present scars.