Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy is applied to study orientation structures of polydimethylsilane (PDMS) films deposited on heteroatom-doped graphite substrates prepared by ion beam doping. The Si Kedge NEXAFS spectra of PDMS show opposite trends of polarization dependence for non irradiated and N-2(+)-irradiated substrates, and show no polarization dependence for an Ar+-irradiated substrate. Based on a theoretical interpretation of the NEXAFS spectra via first-principles calculations, we clarify that PDMS films have lying, standing, and random orientations on the non irradiated, N-2(+)-irradiated, and Ar+-irradiated substrates, respectively. Furthermore, photoemission electron microscopy indicates that the orientation of a PDMS film can be controlled with microstructures on the order of mu m by separating irradiated and non irradiated areas on the graphite surface. These results suggest that surface modification of graphite using ion beam doping is useful for micro-orientation control of organic thin films. (C) 2017 Elsevier B.V. All rights reserved.