The modulation of protein molecular motors (actin-myosin) motility has been tested on several candidate materials for microfluidics devices, all having different hydrophobicities, chemistries and nanotopographies. The analysis of the distribution of molecular properties on the molecular surface of the molecular motor protein suggests that the two very different, temporally separated, conformations of the heads exacerbate the impact of the adsorbing surface on protein behavior. The motility on surfaces with moderate hydrophobicity exhibits a bimodal distribution of velocities of actin filaments, which can be explained by the existence of two molecular conformations of surface-immobilized motor, i.e. with one or two free active heads that propel the actin filament. The study demonstrates that PMMA and not nitrocellulose -the classical choice for actin-myosin motility assays- is the optimum material for the fabrication of future nanofluidics devices based on protein molecular motors.