Atom probe tomography was used to analyze self assembled monolayers of thiophene on different surfaces, including tungsten, platinum, and aluminum, where the tungsten was examined in both pristine and oxidized forms. A glovebag with controlled atmospheres was used to alter the level of oxidation for tungsten. It was shown that different substrates lead to substantial changes in the way thiophene adsorbs on the surface. Furthermore, the oxidation of the surface strongly influenced the adsorption behavior of the thiophene molecules, leading to clear differences in the amounts and compositions of field evaporated ions and molecular ions.