Hydrodynamic approaches are important for biomedical diagnostics, chemical analysis, and a broad range of industrial applications. Size-based separation and sorting is an important tool for these applications. We report the integration of hypersound technology with patterned protein films to provide efficient sorting of microparticles based on particle charge and size. We employed a hypersonic resonator for the acoustic streaming of the fluidic system to generate microvortices that exert drag forces on the objects on the surface that are dictated by their radius of curvature. We demonstrate a size-based sorting of anionic silica particles using protein patterns and gradients fabricated using attractive cationic and repulsive anionic proteins.