The nature of tip sample interaction forces in atomic, force microscopy (AFM) phase imaging strongly affects the resolution of proton conducting domains mapped at the surface of Nafion membranes. Images acquired in repulsive mode overestimated the area of individual proton conducting domains by a factor of 4 (360 vs 90 nm(2)) and underestimated the number of these domains by a factor of 3 (0.9 domains per 1000 nm(2) vs 2.7 domains per 1000 nm(2)) compared to attractive mode. When the cantilever was driven above resonance or when the combination, of scan parameters resulted in an AFM feedback loop that was not fully optimized, phase contrast arose not from proton conducting domains but instead from changes in topography. In attractive mode, phase contrast did not correlate with either topography or changes in topography, and the resulting images most accurately represent the fluorocarbon and aqueous domains at the surface of Nafion membranes.