Nowadays a lot of interest is given to the geometrical modification of heat sink systems to cool down the electronic components. To improve the performance index of the heat sinks, the use of geometrical features with different shapes and at different locations on the surface can be a valuable approach. In this paper, the effect of rectangular shape obstacles on the micro channel heat sink (MCHS) performance is studied. Due to surface features, vortex is developed which helps to increase the heat transfer rate. Numerical modeling software Comsol Multiphysics with heat transfer in fluid physics is used to investigate the characteristics of a micro-channel heat sink. The numerical result shows that the heat transfer rate can be improved through an appropriate arrangement of rectangular shape obstacles, on the heat sink. Numerical analysis and the comparison is carried out for micro-channel heat sink with and without obstacles. In this paper, various parameters like temperature rise, cell Peclet number and Mean effective thermal conductivity are studied.