This paper reports a compact nanostructure based heat sink. The system has an inlet and an outlet valve similar to a conventional heat sink. From the inlet valve, pressurized deionized-water is propelled into a rectangular channel (of dimensions 24mmx59mmx8mm). This rectangular channel houses a nanostructured plate, on which ~600 nm long copper nanorod arrays with an average nanorod diameter of 150 nm are integrated to copper thin film coated on silicon wafer surface. Forced convective heat transfer characteristics of the nanostructured plate are investigated using the experimental setup and compared to the results from a flat plate of copper thin film deposited on silicon substrate. Nanorod arrays act as fins over the plate which enhances the heat transfer from the plate.Excess heat generating small devices are mimicked through a small heat generator placed below the nanostructured plate.Constant heat flux is applied through the heat generator. Thermocouples placed on the heater surface are utilized to gather the surface temperature data. Flow rate and constant heat flux values are varied in order to obtain the correlation between heat removal rate and input power. In this study, it was proved that nanostructured surfaces have the potential to be a useful in cooling of small and excessive heat generating devices such as MEMS (Micro Electro Mechanical Systems) and micro-processors.