Surfaces with controlled micro and nanoscale topographical cues are useful as smart scaffolds and biointerfaces for cell culture. Recently, use of thin-film and surface wrinkling is emerging as a rapid unconventional method for preparing topographically patterned surfaces, especially suited for the production of smart patterns over large area surfaces. On the other hand, there is an increasing interest in employing conducting polymers as soft, biocompatible, conductive biointerfaces or as parts of bioelectronic devices. A novel convenient and versatile method is presented for producing anisotropic topographical cues at the micro- and nanoscale on conducting polymer surfaces. Micro and nanowrinkles were formed during the heat-shrinking process of a thermo-retractable polystyrene substrate. Surface wrinkling was due to the mismatch between the mechanical properties of a conducting polymer ultrathin film and the substrate. Various geometries of wrinkled structures were prepared, demonstrating the tunability of topography depending on the thickness of the conductive film. A method for patterning the conductive properties of the wrinkled substrates was also presented. Such surfaces acted as smart scaffolds for the functional alignment of cells, envisioning their electrical stimulation. Cell adhesion and proliferation were evaluated, comparing different topographies, and a preferential anisotropic alignment of C2C12 murine skeletal muscle cells along wrinkles was demonstrated. The observed trends were also confirmed concerning the formation of aligned myotubes in C2C12 differentiation stage. Furthermore, improved results in terms of aligned and mature myotube formation were obtained by co-culturing C2C12 cells with a fibroblasts feeder layer. The combination of living cells and tunable conductive nanowrinkles will represent a unique tool for the development of innovative biomedical devices.