The nanoscale structure of polytetrafluoroethylene before and after mechanical activation was comprehensively studied by a set of modern physical research methods. The formation of a polydisperse mixture of a mechanically activated fluoropolymer with different molecular weights, the habit of single particles and arbitrary mass, size and morphology of cluster nanostructures was proved by electron microscopy. Two indicators were used to interpret the results of IR spectroscopy: the ratio of the intensities of the band maxima and the half absorption bandwidth. It was revealed that there is an increased concentration of CF2 end groups in the composition of activated polymer, which correspond to the low molecular weight fraction and provide small sizes of its macromolecules. It was proved that filling of polytetrafluoroethylene leads to a decrease in their number, contributing to the formation of a nanostructured polymer with fewer defects. It was established that the combined use of energy exposure and dispersed filler has a positive effect on the physical and mechanical properties of the fluoropolymer. The mechanical activation increases the strength level by 2.6 times and relative elongation by 4.3 times compared to the inactivated polymer; filling the activated polymer with sodium chloride increases the strength level by 2 times and relative elongation by 3.8 times.