An exemplary system suitable for optoelectronics applications, i.e. poly(3-hexylthiophene), hereinafter P3HT, deposited by spin casting onto silicon substrates functionalised by three selected molecules and then properly annealed, has been examined. Grazing Incidence X-ray Scattering (GIXS) measurements have been performed with 4-circle diffractometer, allowing for a fine control of sample axes movement.By choosing different grazing incident angles, diffraction patterns from different layers of polymeric thin films have been recorded. Both in-plane and out-of-plane geometries have been combined in order to obtain complementary structural information. In this way structural and orientational differences of the polymer along with the film thickness (⩽50nm) have been highlighted. For all P3HT films spun on functionalized Si wafer, macromolecular layers close to the substrate surface give some evidence of higher order and orientation than those outmost the surface, and this behaviour is pronounced to a different extent depending on the functionalized molecules used. Contrariwise P3HT layers deposited onto bare Si wafer display reduced orientation and decreased crystallite size, especially at buried interface.