Display omitted •The estimation of temperature upon pulse accumulation shows that a small positive offset is caused by each individual pulse.•Number of pulses needed for LIPSS formation in PS thin films depends on polymer thickness.•Thermal conductivity and diffusivity of supporting substrate influence the onset for LIPSS formation and their quality.•Quality of LIPSS is affected by the substrate optical properties. Here we focus on the influence of both, substrate and film thickness on polymer Laser Induced Periodic Surface Structures (LIPSS) formation in polymer films. For this aim a morphological description of ripples structures generated on spin-coated polystyrene (PS) films by a linearly polarized laser beam with a wavelength of 266nm is presented. The influence of different parameters on the quality and characteristics of the formed laser-induced periodic surface structures (LIPSS) was investigated. We found that well-ordered LIPSS are formed either on PS films thinner than 200nm or thicker than 400nm supported on silicon substrates as well as on thicker free standing films. However less-ordered ripples are formed on silicon supported films with intermediate thicknesses in the range of 200–380nm. The effect of the thermal and optical properties of the substrate on the quality of LIPSS was analyzed. Differences observed in the fluence and number of pulses needed for the onset of surface morphological modifications is explained considering two main effects which are: (1) The temperature increase on polymer surface induced by the action of cumulative laser irradiation and (2) The differences in thermal conductivity between the polymer and the substrate which strongly affect the heat dissipation generated by irradiation.