A study of the formation of Laser Induced Periodic Surface Structures (LIPSS) using near-infrared femtosecond pulsed laser irradiation on poly(ethylene terephthalate) (PET) films deposited over gold substrates has been carried out. We report the influence of the gold substrate roughness and the PET film thickness on LIPSS formation and analyze it in terms of the features of the electric field distribution obtained by computer simulations using COMSOLTM. We obtain LIPSS with periods close to the irradiation wavelength as long as the aforementioned substrate and film parameters remain below certain threshold values, in particular for polymer thicknesses below 200 nm and substrate roughness of few nm. However, experiments show the impossibility of LIPSS formation for rough substrates as well as thick films above these threshold values. In our numerical simulations, we notice the generation of Surface Plasmon Polariton (SPP) in the film-substrate interface that gives rise to a periodical field pattern on the surface of the thin film. This periodicity is broken for a certain level of substrate roughness or film thickness. Moreover, the evolution of the period of the SPP as the substrate roughness and film thickness change for given laser parameters is qualitatively in good agreement with the experimental LIPSS period (below but close to the irradiation laser wavelength). In conclusion, the experimental findings are explained by the formation and behavior of SPP in the thin film-substrate interface. On these grounds, we propose that, for our case of study, this SPP formation and the subsequent inhomogeneous rise in temperature induced by the periodic field on the surface of the sample is the leading mechanism contributing to LIPSS formation.