Sub-monolayer thick films of sexithiophene molecules, vapor-deposited on a set of native silicon oxide substrates with variable surface energy, were investigated using atomic force microscopy. A set of morphological descriptors was chosen and used to describe the formation of molecular islands. This formation is proven to be dependent on the surface energy, specifically linked to the doping concentration of the Silicon wafers. The existence of a concentration range, for which all morphological descriptors change, suggests an interpretation of the surface energy role at the early stage of the film growth different from the one introduced by Bauer for epitaxial growth. Using atomistic theoretical models, we calculated the energy values involved in the process, the number of molecules of the critical nucleus and, for the first time, the step barrier faced by the molecules to ascend, or descend, from the substrate to the island. Step barriers extracted from morphological measurements match with those obtained from molecular dynamics simulations. Our findings indicate that nucleation and island formation in sub-monolayer films on inert substrates are correlated to the surface energy on a molecular scale.