The development of nanoscale lithographic methods on polymer materials is a key requirement to improve the spatial resolution and performance of flexible devices. Here, we report the fabrication of metallic nanostructures down to 20 and 50 nm in size on polymer materials such as polyimide, parylene, SU-8, and PDMS substrates without any resist processing using stencil lithography. Metallic nanodot array analysis of their localized surface plasmon spectra is included. We demonstrate plasmon resonance detection of biotin and streptavidin using a PDMS flexible film with gold nanodots. We also demonstrate the fabrication of metallic nanowires on polyimide substrates with their electrical characteristics showing an ohmic behavior. These results demonstrate high-resolution nanopatterning and device nanofabrication capability of stencil lithography on polymer and flexible substrates.