Micro heat exchangers are among the recent subjects of investigations aiming to achieve high heat dissipation rates from the heat sources such as compact electronic circuits and limit peak temperature levels. This work is an investigation directed towards the design and optimization of micro heat exchangers. Based on the optimization criteria established on scaled up models a micro-heat exchanger made of non-uniform array of silicon square micro pins is designed. The high thermal conductivity of silicon and its compatibility with electronic circuits makes it an excellent candidate used for designing and fabrication on these devices. Finite element models are built and calibrated against the experimental results obtained from tests on macro scale Aluminum specimens in contact with a heat source and facing flowing air at different velocities and different base temperatures in the wind tunnel. Further, the finite element models are extended to the micro level on various geometries and configurations of micro heat exchangers. It was found that square shape pins exhibit the higher heat transfer capability through the device in compare with circular pins in the case of similar hydraulic diameter. In addition for equal contact area between the solid and the fluid, smaller hydraulic diameter for the pins caused larger amount of heat transformation through the solid fluid border. Other important observation is that by using 45{493} attack angle with respect to the fluid direction, higher amount of heat is released by the pins. Also the amount of transferred thermal energy is increasing by diminishing the longitudinal distance between the pins in the direction of the flow.