In this work, we report on the surface patterning of semiconducting poly(3-hexylthiophene) (P3HT) thin films by means of laser-induced periodic surface structures (LIPSS). Two different laser wavelengths, 266 and 532 rim, and a broad range of fluences and number of pulses have been used in order to optimize the LIPSS morphology. Ripples period and depth can be tuned by laser parameters. In particular, the high optical absorption of P3HT at 532 run enables the formation of well-ordered nanostructures with periodicities around 460 nm. Near edge X-ray absorption fine structure (NEXAFS) and Raman spectroscopy reveal a good chemical stability of P3HT thin films during LIPSS formation. Conducting atomic force microscopy (C-AFM) performed on the LIPSS reveals a higher electrical conduction in the trenches than in the ridge regions. Resonance Raman spectroscopy and grazing incidence wide-angle X-ray scattering (GIWAXS) indicate a loss of crystallinity of P3HT thin films during LIPSS formation, suggesting melting of the outer polymer surface. This effect produces ridges with molecular order lower than that of the original thin film. As a consequence of this transformation, the electrical conduction in the ridges becomes lower than that in the trenches.