We consider the mathematical modeling and numerical simulation of high throughput sorting of two different types of biological cells (type I and type II) by a biomedical micro-electro-mechanical system (BioMEMS) whose operating behavior relies on surface acoustic wave (SAW) manipulated fluid flow in a microchannel. The BioMEMS consists of a separation channel with three inflow channels for injection of the carrier fluid and the cells, two outflow channels for separation, and an interdigital transducer (IDT) close to the lateral wall of the separation channel for generation of the SAWs. The cells can be distinguished by fluorescence. The inflow velocities are tuned so that without SAW actuation a cell of type I leaves the device through a designated outflow channel. However, if a cell of type II is detected, the IDT is switched on and the SAWs modify the fluid flow so that the cell leaves the separation channel through the other outflow boundary. The motion of a cell in the carrier fluid is modeled by the Finite Element Immersed Boundary method (FE-IB). Numerical results are presented that illustrate the feasibility of the surface acoustic wave actuated cell sorting approach.