A method for protecting an organic polymer underlayer during a plasma assisted process of depositing a subsequent film on the organic polymer underlayer is disclosed. The method provides the deposition of a protective continuous layer using organic polymer damage-free technique in order to not damage the organic polymer underlayer and to protect the organic polymer underlayer during the plasma assisted process of depositing a subsequent film. The organic polymer damage-free technique is a non-plasma process, using only thermal energy and chemical reactions to deposit the continuous layer. The organic polymer damage-free technique can also be a plasma assisted process using a reduced plasma power low enough in order to not damage the organic polymer underlayer. This method is applicable to many organic polymer underlayers such as organic polymer is aromatic hydrocarbon, polytetrafluoroehtylene (PTFE), parylene, benzocyclobutene-based polymers (BCB), polyimide, fluorinated polyimide, fluorocarbon-based polymers, poly(arylene ether)-based polymers (PAE), cyclohexanone-based polymers, and to many plasma assisted deposition processes such as plasma enhanced CVD deposition, plasma enhanced ALD deposition and plasma enhanced NLD deposition of silicon dioxide, silicon nitride, nitrided diffusion barrier such as TiN, TaN, WN, TiSiN, TaSiN, WSiN.