The performances of organic thin film transistor devices are crucially connected with electronic and structural properties at organic semiconductor/dielectric interfaces. In our studies, Silicon substrates with native SiO2 layer were made hydrophilic according to Radio Corporation of America (RCA) cleaning procedure (RCA treated SiO2, RCA/SiO2) and hydrophobic by following octadecyltrichlorosilane (OTS) modification method (OTS treated SiO2, OTS/SiO2). The surface morphology, molecular orientation and nature of interaction have been studied at rubrene/RCA treated SiO2 and rubrene/OTS treated SiO2 interfaces with increasing thickness of rubrene film from sub-monolayer to multilayer. The angle dependent near edge x-ray absorption fine structure (NEXAFS) spectroscopy and atomic force microscopy (AFM) were used to probe the evolution of molecular configuration and surface morphology of rubrene thin films respectively. The nature of interaction was investigated by X-ray photoemission spectroscopy (XPS) techniques. XPS and NEXAFS studies indicate that the rubrene molecules were physically adsorbed onto both substrates. Angle dependent NEXAFS data suggest that OTS molecules were in standing up configuration on SiO2 surface while rubrene molecules were randomly oriented on both RCA and OTS treated SiO2 substrates. On RCA/SiO2 substrate the percentage of rubrene molecules with twisted backbone was higher compared to that on OTS/SiO2 for 20 nm thick films. The rubrene films were found to grow with different features onto two studied substrates due to their difference in surface energy. At lower coverage, the grain size was larger and nucleation density was smaller onto hydrophilic RCA/SiO2 surface, compared to hydrophobic OTS/SiO2. Hydrophobation of the dielectric substrate surface tends to hinder the diffusion of rubrene molecules resulting in smaller grains for hydrophobic substrate compared to hydrophilic one. (C) 2017 Elsevier B.V. All rights reserved.