The heat transfer and pressure drop characteristics of a straight rectangular and semi cylindrical projections microchannel heat sink were investigated. The heat sinks, made of copper, were aligned in row as a cluster of 21 microchannels, 231 µm wide and 713 µm deep. Water was used as cooling fluid and was made to flow through the channels. A three dimensional analysis was done for Reynolds number ranging between 200 to 1000 with constant heat flux of 106 W/m2 defined relative to the platform area of the heat sink. The temperature rise and pressure drop of the fluid in straight microchannel heat sink was evaluated using ANSYS CFX package and was validated using experimental data. Similar analysis was done for semi cylindrical projections microchannel heat sink by solving the conjugate heat transfer problem. A comparison of heat transfer and pressure drop between rectangular and semi cylindrical projections microchannel was done and the results were laid out. Results shows that heat transfer increases with the use of semi cylindrical projections microchannel heat sink.