The performance of fuel cells is largely dependent on the properties of the membrane electrode assembly (MEA) which consists of a polymer electrolyte membrane and carbon based electrodes. The aim of this work was to obtain new polymer membranes and carbon thin films (for comparison) by Plasma Enhanced Chemical Vapor Deposition (PECVD) and proceed to their physical characterization in order to be able to choose the best conditions that may lead to outstanding proton exchange membranes. The films were deposited on silicon wafers and were analyzed by Scanning Electron Microscopy and Energy Dispersive Spectroscopy (SEM/EDS), Electron Spectroscopy for Chemical Analysis and X-Ray Photoelectron Spectroscopy (ESCA-XPS), Atomic Force Microscopy (AFM), Fourier Transform Infrared Spectroscopy (FTIR) and Rutherford Backscattering Spectrometry (RBS). SEM/EDS and XPS analysis have shown that the chemical composition of the films varied as a function of the plasma (relative percentages of the reactant gases CH4 and SF6) while variation of the pressure and RF power did not have a marked effect on the topographic quality and composition of the membranes. AFM analysis, as well as SEM, made possible to observe the topography of the membranes showing that the films are very smooth with some localized defects. Futhermore, AFM micrographs have shown that the roughness (root mean square - RMS) of the membranes have peak to valley differences in the order of some nanometers. RBS and Profilometer techniques indicated that the deposition rate of the films is not linearly dependent on the plasma composition while FTIR spectroscopy has shown the presence of the perfluorinated sulphonate groups.