A plasma treatment on PDMS (polydimethylsiloxane) is a useful way to modify its surface properties. Plasma treatments using oxygen or argon on the surface of PDMS prior to the parylene C deposition show dramatic improvement of film clarity and surface morphologies. Even mild oxidation on PDMS using an argon plasma treatment showed some improvement as similar to strong oxidation with oxygen plasma. The silica-like layer is produced on PDMS surface by plasma treatments, and this brittle, wettable layer can make the subsequent parylene coating transparent and unwrinkled. It also improved mechanical performances of the bi-layer coatings, as compared to those of individual constituents. In an effort to better understand the mechanism(s) of the plasma treatments that has resulted in the desirable interfacial structure and properties, the mechanical performance and microstructural characterization of the polymer bi-layer coatings were systematically examined via a dynamic nanoindentation, atomic force microscope (AFM), and scanning electron microscope (SEM). Accordingly, this study presents a means of developing a parylene/PDMS bi-layer with much enhanced protection capability while retaining compliance from PDMS for advanced packaging applications.