One of the major limitations of flexible sensors is the loss of conductivity upon multiple stretching and bending cycles. Conducting fillers with two different geometries, carbon black and carbon nanotubes, were introduced in polydimethylsiloxane (PDMS) for physical insights into the structure formation of nanofillers by the application of periodic tensile stress. The loading of the nanofillers was selected beyond the percolation threshold to determine the cyclic stability of the resulting network channels. The surface chemistry of carbon nanotubes has been varied to understand the interfacial interactions at the molecular length scale. The combination of in situ stretching, annealing, and vis-à-vis conductometry of nanocomposite films with synchrotron-based ultra-small angle X-ray scattering experiments enables us to highlight the importance of the fractal dimensions of nanofillers for the molecular level interactions. The irreversible formation of nanofiller network geometries under cyclic stress and annealing was found to be responsible for the electrical properties of a flexible conducting film.