This study numerically investigates the feasibility and advantages of using a multilayer pin-fin heat sink to increase the overall performance of the heat sink. For the purpose of determining overall performance of the pin-fin heat sink a figure of merit (FOM) term is introduced in this paper, which constituted of both the thermal resistance and the pumping power of the heat sink. Higher the FOM of a heat sink better is its overall performance. A computational fluid dynamics software CoventorWARE™ is used for the analysis of micro heat sink performance. A small portion of the entire heat sink is modeled in this study assuming repeatability towards both sides for the ease of analysis. The developed models consist of two sections, the substrate (silicon) and the fluid (water at 278K). A uniform heat flux is applied to the base of the heat sink. A single layer micro pin-fin heat sinks with same dimensions as of the multi layer heat sink was also modeled for the comparison purpose. Temperature distribution at five different locations from the inlet to the outlet section is also analyzed to study the temperature distribution over the heat sink. Circular pin-fins were used in both the multilayer and single layer micro heat sinks. Feasibility of using micro channels as the second layer was also investigated in this paper and it proved to have advantages over using pin-fin structures on both layers. A geometric optimization based on the substrate thickness of the second layer of the double layer heat sink showed that the substrate thickness of the second layer doesn't have any effect on the overall thermal resistance of the heat sink.