Biofouling is one of the most critical problems which plaques all biosensing devices operating in fluid media. Acoustic streaming phenomena has the potential to eliminate biofouling; however, the microscopic mechanism of streaming induced non-specific protein removal is largely unknown. In this work, a novel multiscale simulation model is developed to evaluate the effects of acoustic streaming flow on a functionalized nanoparticle typically employed in biosensing applications. First, we investigate a finite element fluid solid interaction (FE-FSI) model of acoustic streaming phenomenon resulting from the interaction of surface acoustic waves (Rayleigh mode) with liquid loading is developed. The fluid-velocity fields are imposed as boundary conditions in an atomistic simulation model to evaluate the effects of streaming velocity fields on the protein molecule attached to a nanoparticle sensing material. The multi-scale model would provide insights into the dynamics of fluid flow and the interplay of various fluid induced adhesive and removal forces at the atomistic level which is critical for efficient removal of non-specifically-bound proteins from the biosensor surface.