A MEMS-based active system is currently under development for flow separation control in the transonic regime. The system consists of micro shear stress sensors for flow sensing and micro balloon actuators for separation control. We have successfully completed the first phase of the program in which the micro sensors and actuators were fabricated and tested in a wind tunnel facility. In the test, the sensors and actuators were flush mounted on a 3D model, which is representative of the upper surface of a wing with a deflected trailing edge flap. The model was installed in the wind tunnel and tested at a series of Mach numbers between 0.2 and 0.6. For all Mach numbers, the sensor output indicates that flow separates over the trailing edge when the micro balloons are in the ‘down’ position. When the micro balloons are inflated, the shear stress level on the trailing edge increases substantially, indicating an improvement of the separation characteristics. This result demonstrates the feasibility of using MEMS sensors and actuators to control flow separation. It is the first step toward the development of a revolutionary closed loop flow control system applicable to existing and future aircraft to enhance aerodynamic performance.