James, the rust should wear off on its own; however, if it were my car and the rust appeared fairly heavy I'd use some fine steel wool to remove as much of the rust film as possible rather than foul up the new brake pads. If the rust is causing the brakes to pulse it must be quite heavy. Rusted rotors are common on pre-owned cars on the MB dealers' lots. You may even notice a light rust film on the rotors after washing your car.

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Fred Hoelzle