The aim of this work is to investigate the selective adsorption of ultra-thin organic films on model heterogeneous aluminum-copper surfaces via self-assembly from mixed monomer solutions. Patterned aluminum/copper substrates were prepared via microsphere lithography by means of sequential physical vapour deposition of the respective metal films on silicon wafers. The formation of monolayers with a methylene end group on the bi-metallic surfaces was performed from a dilute cocktail solution of two organic molecules with thiol and phosphonic acid head groups. The ordering of the monolayers was analyzed by means of Polarization Modulated-Infrared Reflection Absorption Spectroscopy (PM-IRRAS). Imaging Time-of-Flight Secondary Ion Mass Spectroscopy (ToF-SIMS) experiments were performed to analyze the lateral distribution of the two mono-functional molecules. The preferred adsorption sites of the functionalities in the cocktail solution reproduced the patterned image of the model substrate with chemical contrast. The copper regions were covered with monolayers of thiol head group and organophosophonic acid monolayer was detected on aluminum regions. This self-localization of the organofunctional molecules converted the heterogeneous surface of the patterned substrate to a surface uniformly covered with methyl terminated self-assembled monolayers (SAMs). (C) 2013 Elsevier B.V. All rights reserved.