The present paper describes the influence of the chemical structure of two aminoalkoxysilanes: 3-aminopropyltriethoxysilane (APTS) and N-(3-(trimethoxysilyl)-propyl)-ethylenediamine (TSPEN) on the morphology of thin layer hybrid films with phosphotungstic acid (HPW), a Keggin heteropolyanion. X-ray photoelectron spectroscopy analyses indicated that both silane films showed protonated amine species interacting with the heteropolyanion by electrostatic forces as well as the presence of secondary carbamate anions. The hybrid films have different surface morphology according to atomic force microscopy analyses. The hybrid film with TSPEN forms flatter surfaces than the hybrid film with APTS. This effect is ascribed to higher flexibility and chelating ability of the TSPEN on adsorbed molecules. Ultrasonication effect on surface morphology of the hybrid film with APTS plays a fundamental role on surface roughness delivering enough energy to promote surface diffusion of the HPW heteropolyanions. This diffusion results in agglomerate formation, which corroborates with the assumption of electrostatic bonding between the HPW heteropolyanions and the protonated amine surface. These hybrid films could be used for electrochemical sensor design or to build photochromic and electrochromic multilayers. (c) 2011 Elsevier B.V. All rights reserved.