In this work, the structure and conductive structure of perfluorinated sulfonated ionomers were investigated by tapping mode, material sensitive atomic force microscopy (AFM). At cross section of membranes, large ordered lamellar-like areas were found. From adhesion force mappings, approximately 50 nm large water-rich areas could be identified by their low adhesion. These areas were interpreted as ionically conductive phase. They appeared circular and isolated before any forced current flow through the sample (activation). After activation, branched, long and flat ionically conductive phase structures in direction of applied voltage were found. They were interpreted as the formation of a continuous ionically conducting network formed by the current flow. In a second part, the material sensitive imaging was used to analyze the distribution of ionomer and platinum covered carbon particles in fuel cell electrodes. The analysis was based on the high adhesion of ionomers compared to the carbon supported catalyst particles.