The study is based on an analysis of MEMS heat exchanger of three different geometries: wavy, triangular and rectangular using water, air and different types of refrigerants as test fluids. The problem is solved using finite element method. The aim of this analysis is to evaluate the performance of MEMS heat exchanger for different geometries and to obtain an optimum design for better heat transfer enhancement. It is apparent from this work that rectangular surface heat exchanger shows the best performance for heat transfer enhancement technique in comparison to other geometries. Moreover, it is also easy to manufacture. Therefore, the rectangular surface may be used instead of other configurations of heat transfer surfaces. In this analysis, emphasis is given on increasing heat transfer area of MEMS heat exchanger by reducing the pitch which shows that 0.475 mm is the optimum pitch as further decrease of pitch length does not have any significant effect on the effectiveness and heat transfer.