1st remedy, parang first aid, is to apply rust converter. Meron nabibili nyan sa hardware like ace or handyman. A common brand is Ospho rust converter. Just try to remove the rust flakes, then clean with water. Apply the rust converter with a brush and let it soak. The rust will turn to a blackish color. That is ferous sulphate, a very hard surface that will serve as a shield to further rusts since oxygen can no longer attack the metal. Wash it again with water, let dry, and then apply a coating of base paint. Do not use lead oxide paint since lead oxide will just lead to more rust.
next step is to apply rubberized undercoat to prevent rusting underneath. It is also best to apply rust converter at rusted areas before applying undercoating.
last resort of course is to replace the plates of the flooring. This is normally done by your car body repair shops. Pero kung makapal pa naman at naagad mo ng rust converter e tatagal pa yan.