A lot of interest is given to the geometrical modification of heat sink systems. To improve the performance of heat sinks, the use of surface features with different shapes and at different locations on the surface can be a valuable approach. In this paper, effect of rectangular shape obstacles, on the heat sink 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 analyze 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 is carried out for micro-channel with and without obstacles. In this paper, various parameters like temperature rise, cell Peclet number, and Mean effective thermal conductivity studied.