The surface morphology of a proton-conducting polymer membrane is modified by plasma treatments in view of electrochemical applications. The atmospheric-pressure glow plasmas generated using helium/hydrogen gas mixtures, or helium as the working gas are etching the surfaces very efficiently. The Nafion membranes placed between two dielectric disks undergo morphological, as well as surface chemical structural changes during exposure to the RF powered discharges. The change in the surface morphology depends on the composition of the plasma. The electrochemical cell employing the modified membrane as the electrolyte displays remarkable improvements in registering the current density.