Methods of processing a substrate so as to protect an active area include positioning a substrate in an inductively coupled plasma processing chamber, supplying process gas to the chamber, generating plasma from the process gas and processing the substrate so as to protect the active area by maintaining a plasma potential of about 5 to 15 volts at the substrate surface and/or passivating the active area by using a siliane-free process gas including at least one additive effective to form a protective layer on the active area of the substrate, wherein the protective layer includes at least oneelement from the additive which is already present in the active area.