A method of fabricating templated semiconductor nanowires on a surface of a semiconductor substrate for use in semiconductor device applications is provided. The method includes controlling the spatial placement of the semiconductor nanowires by using an oxygen reactive seed material. The present invention also provides semiconductor structures including semiconductor nanowires. In yet another embodiment, patterning of a compound semiconductor substrate or other like substrate which is capable of forming a compound semiconductor alloy with an oxygen reactive element during a subsequent annealing step is provided. This embodiment provides a patterned substrate that can be used in various applications including, for example, in semiconductor device manufacturing, optoelectronic device manufacturing and solar cell device manufacturing.