The Au nanoparticle monolayer is formed by self-assembly technology on the Si substrates terminated with different functional groups. Silicon nanotips were fabricated by a self-assembled gold colloidal particle monolayer as an etch mask. The silicon nanotips with high density and uniformity in height and shape were obtained using reactive ion etching (RIE). The Si nanotips on the surface of the 3-aminopropyltrimethoxysilane (APTMS)-treated Si substrate are less-ordered array and uniformity than 3-mercaptopropyltrimethoxysilane (MPTMS)-treated Si substrate at the same etching conditions. The ordered array and uniformity of Si nanotips on the APTMS-modified Si substrate was improved through heat-treatment. This result is implied the different functional groups on the Si surfaces could affect the formation of the Si nanostructures during RIE process. The uniformly nanotip pattern with height of >20 nm is obtained on the etched nanoparticle-coated Si substrate. This method can be applied to patterning a wide variety of thin film materials into tip arrays.