Features of the fine structure of three samples of perfluorinated Nafion® type membranes—Nafion-115, its Russian analogue MF-4SK, and a new similar material PFM-E produced according to our novel water-emulsion technique—have been characterized using the small-angle neutron scattering technique. A difference in the regularity of common elements of fine structure (cylindrical channels) in the membranes has been revealed. Nafion-115 has the most regular structure with a diffraction peak corresponding to the double channel diameter and an additional broad maximum in the scattering curve indicating a long-range order in the arrangement of straight cylindrical channels. For MF-4SK, in addition, twisted and less ordered channels have been observed. In the PFM-E sample channels have a tortuous and branched structure with diameters similar to Nafion-115. Only a short-range order (40–50 Å) in the arrangement of the channels has been detected, and correlation in their mutual orientation at longer distances is weakened. It has been supposed that the observed branched structure of the channels promotes an increase in water content and an improvement in proton conductivity.