Biomedical devices are moving towards the incorporation of nanostructures to investigate the interactions of biological species with such topological surfaces found in nature. Good optical transparency and sealing properties, low fabrication cost, fast design realization times, and biocompatibility make polymers excellent candidates for the production of surfaces containing such nanometric structures. In this work, a method for the production of nanostructures in free-standing sheets of different thermoplastic polymers is presented, with a view to using these substrates in biomedical cell-surface applications where optical microscopy techniques are required. The process conditions for the production of these structures in poly(methyl methacrylate), poly(ethylene naphthalate), poly(lactic acid), poly(styrene), and poly(ethyl ether ketone) are given. The fabrication method used is based on a modified nanoimprint lithography (NIL) technique using silicon based moulds, fabricated via reactive ion etching or focused ion beam lithography, to emboss nanostructures into the surface of the biologically compatible thermoplastic polymers. The method presented here is designed to faithfully replicate the nanostructures in the mould while maximising the mould lifetime. Examples of polymer replicas with nanostructures of different topographies are presented in poly(methyl methacrylate), including nanostructures for use in cell-surface interactions and nanostructure-containing microfluidic devices.