We investigated the controlled fabrication of uniform vertical aligned silicon nanowires with desired length, diameter and location by combining nanosphere lithograph and metal assisted chemical etching techniques. The close-packed polystyrene nanospheres array was obtained by self-assemble technique, followed by reactive ion etching to acquire a non-close-packed monolayer template. Subsequently, the template was used to create a metal film with nanoholes array, which enable the controlled fabrication of ordered silicon nanowires via metal assisted chemical etching technique. By adjusting the monolayer of polystyrene nanospheres and the conditions for the metal assisted chemical etching, we obtained uniform distributed silicon nanowires with desired morphology. The aspect ratio of the silicon nanowires can reach to about 86:1. Furthermore, we have obtained the double-layer silicon nanowires by slight modifying the process. The influences of various conditions during etching were also discussed for improving the controlled fabrication.