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Nonspecific binding is a universal problem that reduces bioassay sensitivity and specificity. We demonstrate that ultrasonic waves, generated by 5-MHz quartz crystal resonators, accelerate nonspecifically bound protein desorption from sensing and nonsensing areas of micropatterned protein arrays, controllably and nondestructively cleaning the micropatterns. Nonsensing area fluorescent intensity values dropped by more than 85% and sensing area fluorescent intensity dropped 77% due to nonspecific binding removal at an input power of 14 W. After patterning, antibody films were many layers thick with nonspecifically bound protein, and aggregates obscured patterns. Quartz crystal resonators removed excess antibody layers and aggregates leaving highly uniform films, as evidenced by smaller spatial variations in fluorescent intensity and atomic force microscope surface roughness values. Fluorescent intensity values obtained after 14-W QCR operation were more repeatable and uniform.