Here we report X-ray Photoelectron Spectroscopy (XPS), Secondary Ion Mass Spectrometry (SIMS) and Atomic Force Microscopy (AFM) studies of 3-aminopropyltrimethoxysilane (APTMS) film on a silicon oxide substrate. It was intended to verify the structure at macro-, micro(-) and nano-levels of the self-assembled monolayers obtained to identify the factors affecting possible film defects and to optimise the deposition technique. A method, involving the removal of the native SiO2 surface layer by a HF/NH4F solution followed by the generation of a new layer of silicon oxide by a NH4OH-H2O2 Solution, was preferred. The N(1s) XPS maps highlighted good macroscopic film homogeneity confirming a complete coating of the substrate. SIMS analyses involving depth profiles for both positive (H+, O+, Si+, C+) and negative (H-, O-, CN-, C-2(-)) secondary ions and chemical maps for H-, O-, CN- ions indicated a high molecular order for the APTMS chains and suggested the presence of a thin water layer adsorbed at the surface of the self-assembled film. An approximate APTMS thickness estimate was also provided by Stopping Range of Ions in Matter calculations. AFM investigations carried out on several areas of the samples showed flat and regular surfaces. (c) 2005 Elsevier B.V. All rights reserved.