Anodic aluminum oxide (AAO) nanopores are excellent templates to fabricate different nanostructures. However, the pores are limited to a hexagonal arrangement with a domain size of a few micrometers.  In this dissertation, focused ion beam (FIB) is used to create pre-patterned concaves to guide the anodization. Due to the advantage of FIB lithography, highly ordered AAO arrays with different arrangements, alternating diameters, and periodic pore densities are successfully achieved. Anodization window to fabricate ordered AAO is enlarged due to the FIB pre-pattern guidance. AAO has also been successfully used as a template to nanoimprint prepolymer to synthesize vertically aligned and high aspect ratio h-PDMS nanorod arrays with Moiré pattern arrangements.

The formation mechanism of anodic TiO2 nanotubes is proposed in this dissertation. Moreover, FIB pre-pattern guided anodization is introduced to synthesize highly ordered TiO₂ nanotubes with different morphologies. The effects of inter-tube distance and arrangement to the structure of TiO₂ nanotubes are investigated. TiO2 nanotubes with branched and bamboo-type structures are achieved by adjusting anodization voltage. The influence of patterned concave depth and surface curvature on the growth of TiO₂ nanotubes and AAO are studied. The efficiency of TiO₂ nanotubes in supercapacitors and photoelectrochemical water splitting are optimized by enlarging surface area and increasing electrical conductivity.

Focused ion beam can not only create concave arrays to guide the electrochemical anodization, but also be used for nanoscale sculpting and 3D analysis. When the TiO₂ nanotube surface is bombarded by FIB, there is a mass transfers due to ion-induced viscous flow and sputter milling, thus the TiO₂ nanotubes are selectively closed and opened. By combining FIB cutting and SEM imaging to create a series of 2D cross section SEM images, 3D reconstruction can be obtained by stacking SEM images together. This 3D reconstruction offers an opportunity to directly and quantitatively observe the pore evolution to understand the sintering process.