The thesis describes a novel process to selectively close and open certain region of an anodic alumina nanochannel array by bombarding its surface with high and low energy focused-ion-beam respectively. This ion induced gating technique provides a platform for the selective growth of different materials into different regions of a nanochannel array and facilitates the fabrication of multi-element nanowire arrays on an anodic alumina substrate. Since this unique substrate, which has self-aligned nanochannels of extremely high aspect ratio, is being extensively exploited for the fabrication of ultra high density magnetic recording medium, surface enhanced Raman substrates, metamaterials with unusual optical properties, and nanocomposites with multiple elements, etc., a successful process opens up numerous possibilities for the creation of nanowire arrays with desired geometry.