AFM methods were applied to resolve the surface and near-surface morphology of the ionic domains in Nafion membranes, Surlyn ionomers, and other ionomers. The ionic dusters were resolved by a new tapping AFM method where low oscillation amplitudes were used, and tip-ionic domain interactions were apparently able to dominate the signal allowing nanometer-level resolution of the domains. In other operating modes, the fluoropolymer crystal or aggregate domains were imaged using tapping AFM by the normal "stiffness" contrast. By sequential images taken under different AFM conditions, the "softer" fluorine-depleted regions were found to contain ionic domains in the, same topographical areas, and the changes due to swelling by water were examined in one ease. A third AFM operating mode was used to examine the composition in the outermost few angstroms of the surface. Data proving the existence of a very thin fluorine-rich "barrier" layer covering the entire surface of Nafion are obtained, and its relevance to vapor-versus liquid water penetration is discussed.