This paper will present fabrication challenges for a complicated micro channel system at low temperature process by MEMS techniques. This channel will be integrated with an array of temperature sensors and a set of heaters for the purpose of study on the micro-scale heat transfer inside. The heat transfer results may provide a clue whether the microchannel cooling process can be used to solve the future cooling problem encountered in an extremely high power density CPU chip. Design and fabrication challenges encountered in this processes are discussed. A final measurement for the validation of the heaters and the sensors fabricated and a study of the heat transfer coefficient distributions inside the micro channel are also presented.