Cathodic DC plasma deposited films have shown promise as intermediate adhesion and barrier layers for use in the interface engineering of corrosion protection systems on various materials. The surface treatment of plasma deposited trimethylsilane (TMS) films with various post-deposition plasma treatments can improve the adhesion of various paints to these films, which are usually strongly adhered to underlying substrates. Research into the application of these systems for corrosion protection of aluminum alloys included post-deposition treatments of the TMS films with hexafluoroethane (HFE) plasmas, which was seen to significantly improve the adhesion of primers. Oxygen plasma cleaning of the alloy surfaces, prior to deposition of the TMS film, is normally employed to remove organic contaminants. During testing of sample aluminum panels, one batch was processed without the oxygen plasma treatment and exhibited extensive adhesion failures. The investigation of these results shows that low levels of fluorocarbon contaminants readily react with the alloy surface and deposit a fluorine containing carbonaceous layer, which dramatically interferes with the adhesion of the plasma polymer to the alloys, but the adhesion with primer coatings remains tenacious. X-ray photoelectron spectroscopy (XPS) studies also show that the presence of even low levels of these contaminants in the chamber, during the oxygen cleaning process, is sufficient to induce the conversion of the surface from oxide to a mixture of oxide and fluoride. This conversion is considered detrimental to the corrosion resistance of these systems.