Titania nanostructures have been prepared by anodisation in aqueous solution assisted by focused ion beam (FIB) milling. The structures formed are bi-periodic, a disordered “native” nanotube array, with characteristics similar to those formed by the standard anodisation process and an ordered array of tubes with larger diameters, guided by the positioning of the FIB concave pits. Low kV EDX analysis shows implanted Ga in FIB-treated titanium which is efficiently removed by the anodisation process. Following thermal annealing, the FIB-treated regions also crystallise to the same anatase phase as the native regions. This result is in stark contrast to previous FIB-assisted anodisation studies which only produced nanostructured arrays of native dimensions. This singularity is discussed in terms of the stable FIB-induced crystalline defects which, in an aqueous electrolyte, can result in the growth of a weaker barrier layer and larger tubes. This novel process gave hexagonal and square arrays with tailored cross-sectional dimensions and therefore has potential for the synthesis of novel meta-materials.