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A MEMS-based sensor and actuator system has been designed and fabricated for separation control in the compressible flow regime. The MEMS sensors in the system are surface-micromachined shear stress sensors and the actuators are bulk-micromachined balloon vortex generators (VGs). A three-dimensional (3-D) wing model embedded with the shear stress sensors and balloon VGs was tested in a transonic wind tunnel to evaluate the performance of the control system in a range of Mach number between 0.2 and 0.6. At each Mach number tested, the shear stress sensors quantify the boundary layer on the surface of the wing model while the balloon VGs interact with the boundary layer in an attempt to provide flow control. The shear stress measurements indicate the presence of a separated flow on the trailing ramp section of the wing model at all Mach numbers tested when the balloon VGs are not activated. This result is confirmed by total pressure measurements downstream from the wing model where a wake profile is observed. When the balloon VGs are activated, the shear stress level on the trailing ramp increases with the Mach number. At the highest Mach number tested, this increase elevates the shear stress on the ramp to almost the same level as the unseparated flow, suggesting the possibility of a boundary layer reattachment. This result is supported by the downstream pressure measurements which show a large pressure recovery when the balloon VGs are activated. The wind tunnel experiment successfully demonstrated two aspects of the MEMS flow control system: the effectiveness of the microshear stress sensors in measuring the separation characteristics of a high-speed compressible flow and the ability of the microballoons in positively enhancing the aerodynamic performance of a high-speed wing through boundary layer modification.