Non-specific binding is an ongoing problem that dramatically reduces the sensitivity and selectivity of biosensors. We demonstrate that ultrasonic waves generated by surface acoustic wave (SAW) devices remove nonspecifically bound proteins from the sensing and non-sensing regions of the micropatterns. Our approach is proven for controllably and non-destructively cleaning the sensor interface to recover signals from a fouled background. In this work, 128^o YX lithium niobate was chosen for its high coupling coefficient and efficient power transfer to mechanical motion. Ultrasonic waves propagating along the surface were coupled into a microfluidic cell containing both specifically bound and non-specifically bound proteins. Fluorescence intensity was used to assess cleaning efficacy of the micropatterns. Our results have shown that excess protein layers and aggregates are removed leaving highly uniform films as evidenced by fluorescent intensity profiles. Selected antigen-receptor interactions remained bound during the acoustic cleaning process and retained their efficacy for subsequent antigen capture. Results demonstrate proper fluorescent signal recovery for both the sensing and nonsensing regions of the micropatterns. Of significance is that our approach can be integrated into existing array technologies where sensing and nonsensing regions are extensively fouled. We believe that this technology will be pivotal in the development and advancement of microfluidic devices and applications.