In the present work, a special microcontroller-based data acquisition and control system was designed and fabricated, for fast and accurate flow measurements with programmable modes of operation. The system can apply predetermined power to the heater and simultaneously is able of monitoring both the thermopile signal and the heater current. An RS232 connection was also implemented for the communication with the outside world. The interface circuit was adapted to the micromechanical flow sensor for evaluation. Various sensor parameters were extracted in both laminar and turbulent flow conditions. The sensor responses with three operation modes (constant voltage, power and temperature) were also obtained.