Methods and apparatus to form films on sensitive substrates while preventing damage to the sensitive substrate are provided herein. In certain embodiments, methods involve forming a bilayer film on a sensitive substrate that both protects the underlying substrate from damage and possesses desired electrical properties. Also provided are methods and apparatus for evaluating and optimizing the films, including methods to evaluate the amount of substrate damage resulting from a particular deposition process and methods to determine the minimum thickness of a protective layer. The methods and apparatus described herein may be used to deposit films on a variety of sensitive materials such as silicon, cobalt, germanium-antimony-tellerium, silicon-germanium, silicon nitride, silicon carbide, tungsten, titanium, tantalum, chromium, nickel, palladium, ruthenium, or silicon oxide.