With the advancements of technology, employment of micro-electronic devices is increasing everyday. Because of extreme compaction, these devices encounter high temperatures. Increase of temperature results in the decrease of durability; Therefore, cooling is an important issue. Many approaches are presented in order to solve this problem. One of the most effective alternatives is using micro-channels that are mounted on these devices. The channels are constituted by solids with high conductivity through which coolant is flown. Obviously, many parameters are involved in the design and performance of micro-heat exchangers. Consequently, experiments and analyses of one of them is costly and time consuming. Hence, one appropriate way is numerical simulation. In this work, rectangular micro-channels are simulated and analyzed. Subsequently, temperature distribution, distribution of thermal flux, pressure gradient and the temperature of micro-electronic devices in single and multi layered micro-channels are analyzed and their thermal resistances are compared. The results show better performance of this approach compared with single layered one. Finally, the effects of the number of layers, pump strength, the coolant inlet velocity, Reynolds number, the aspect ratio and the mass flow inlet are analyzed on the thermal resistances of rectangular micro-channels. Some suggestions are made to improve the introduced system.