We report on the fabrication of gold coated nanostructured polymer thin films and on their characterization as substrates for surface enhanced Raman spectroscopy (SERS). Laser induced periodic surface structures (LIPSS) were obtained on thin polymer films of poly(trimethylene terephthalate) (PTT) upon laser irradiation with the fourth harmonic of a Nd:YAG laser (266 nm, pulse duration 6 ns) resulting in a period close to the incident wavelength. The nanostructured polymer substrates were coated with a nanoparticle assembled gold layer by pulsed laser deposition using the fifth harmonic of a Nd:YAG laser (213 nm, pulse duration 15 ns). Different deposition times resulted in thicknesses from a few nanometres up to several tens of nanometres. Analysis by atomic force microscopy and grazing incident small angle X-ray scattering showed that gold coating preserved the LIPSS relief. The capabilities of the produced nanostructures as substrates for SERS have been investigated using benzenethiol as a test molecule. The SERS signal is substantially larger than that observed for a gold-coated flat substrate. Advantages of this new type of SERS substrates are discussed.