Nafion inside Polymer Electrolyte Membrane Fuel Cells (PEMFC) catalyst layers can be found as an ultra-thin film coating the catalyst and the catalyst support surfaces. Nafion morphology shows to be strongly sensitive to the type of material where the film is deposited, especially the hydrophobic/philic character of these materials. Our work consists in performing a complete investigation of the substrate hydrophilicity effects on the physical properties of Nafion ultra-thin film at different hydration levels. We investigate in a unique framework a variety of environments peculiar of the PEMFC catalyst layer, ranging from hydrophobic (carbon) to hydrophilic (platinum) substrates. The numerical method chosen for this work is classical Molecular Dynamics simulations. The well-thermalized thin-film configurations were described in details in terms of their structural and dynamical properties.