In this paper, a novel design of silicon micro/nanopillars based multilayer water-cooled heat sink is presented, which enhances the overall thermal performance of electronics/MEMS components by a noteworthy amount. Heat dissipation rate of electronic devices is significantly increased by the silicon micro/nanopillars, which are grown in the microchannels by utilizing the micromasking effect in deep reactive ion etching. Due to the smaller diameter (0.5–2 μm) and larger height (∼100 μm), the surface area of these silicon pillars is very high, which results in enhanced convective heat transfer rate, and thus improved thermal performance. Gold thin films of varying thicknesses were used as etching mask during the fabrication of silicon microchannel and silicon nanopillars. Effects of etching mask type, mask thickness, platen power and substrate temperature on controlling the physical dimensions and the density of silicon pillars in the microchannels, are presented. A simple thermal model is developed to compare the heat dissipation characteristics of the heat sink, with and without the silicon pillars. The analytical analysis shows that the heat dissipation rate of the heat sink with silicon pillars can be increased by 16% than that of without silicon pillars. The effects of pillar diameter, height, and pillar density, on overall thermal resistance and the heat dissipation rate are also shown.