In this paper, we present recent work from our group focussed on the fabrication of nanopore and nanotube arrays using self-ordered electrochemistry, and their application in several key areas including template synthesis, molecular separation, optical sensing, and drug delivery. We have fabricated nanoporous anodic aluminium oxide (AAO) with controlled pore dimensions (20–200 nm) and shapes, and used them as templates for the preparation of gold nanorod/nanotube arrays and gold nanotube membranes with characteristic properties such as surface enhanced Raman scattering and selective molecular transport. The application of AAO nanopores as a sensing platform for reflective interferometric detection is demonstrated. Finally, a drug release study on fabricated titania nanotubes confirms their potential for implantable drug delivery applications.