In this work, we report on the synthesis and characteristics of composite membranes consisting of polymeric porous supports coated with thin films. Polyethylene terephthalate track etched membranes were used as porous substrates, while chemically-resistant polytetrafluoroethylene-like thin films were obtained by magnetron sputtering deposition. The effects of coating process on topside, backside and inside pores surfaces, leading to changes of morphology and chemical composition at surface were investigated upon the deposition time. Scanning Electron Microscopy (SEM) was used to reveal the morphological characteristics. The chemical composition of the initial support and resulted composite membranes was determined by means of Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Photoelectron Spectroscopy (XPS) measurements, where the chemical groups containing fluorine were used as indicators for plasma species penetration inside pores. Process conditions were identified which lead to membranes with contrast of properties on their sides, or completely coated with Teflon-like material on both sides and inside pores, thus with various wettability and liquid flow properties.