The influence of the preparation conditions, including substrate functionalization with common silanizers, onto structure/morphology of the overlying poly(3-hexylthiophene) thin films has been investigated by using both grazing incidence X-ray diffraction and atomic force microscopy. The factors determining the formation of spin-coated films suitable for applications in field effect transistors, i.e. concentration, spin-speed, and thermal treatment are addressed. We have established, by a tuning of the preparation and post-deposition treatments, the optimal conditions to get films with the required structural/morphologic features. Moreover we have shown that the macromolecules orient and organize at the interface zone (⩽10 nm from the interface) better than in the upper layers, i.e. far away from the interface.