One of the effective liquid cooling techniques for microelectronic devices is attaching micro channel heat sink to the inactive side of chip. A micro channel heat sink is a device that decreases temperature by flowing coolant through micro channels. The present study focuses on the conjugate heat transfer analyses for different cross-sections (trapezoidal, hexagonal, octagonal and circular).After present study is validated with the published result in the literature, the comparative study of parallel and counter flow configuration is performed. Different geometries are modeled using CATIA V5 software and simulated in ANSYS Fluent R14. From these CFD simulations, preferred configuration of parallel-flow or counter-flow is chosen based on maximum possible heat transfer for effective cooling. The focus on the analyses is to improve the heat transfer rate by either decreasing the chip wall (bottom wall) temperature or the decrease in overall thermal resistance. © 2016, Global Digital Central. All rights reserved.