The deposition of silicon alloys for protective and optical coatings on polymers is of increasing interest. The understanding of the plasma polymer interaction is of prime importance here. In this work, we report a study of the influence of N-2, H-2, and O-2 plasma treatments on pure and commercial grade polycarbonate (PC) in order to enhance the adhesion of plasma deposited silica films. Treatments and depositions were carried out in a low pressure (1 mTorr range) integrated distributed 2.45 GHz microwave electron cyclotron resonance reactor, which allows the deposition of dense stoechiometric silica at room temperature. The plasma-polymer interaction is studied by in situ UV-visible spectroscopic ellipsometry on thin spin-coated PC films. The absorption in the PC layer was found to increase in the UV which was attributed to the different reaction products of photo-Fries rearrangements, especially for pure PC. Gel permeation chromatography measurements showed that the major influence of plasma treatment on pure polycarbonate is chain scission opposed to crosslinking in the case of commercial grade PC, indicating that additives present in commercial grade PC play a major role in the crosslinking mechanisms. The plasma treatment modifies the top 330 nm/homogeneously and no indication of a high index surface layer (50-200 nm) or gradient was found. This is attributed to the low pressure of the plasma treatment, which makes a redeposition of volatile organic species unlikely.