A modified nanosphere lithographic process for producing high aspect ratio and size-tunable nanopore arrays is described. A self-assembled bilayer nanosphere template is created as an etch mask for a deep reactive ion etching (DRIE) process. The size of the nanopores is tuned by reducing the diameter of the top-layer nanospheres using oxygen etching. Nanopore arrays with mean in-plane widths ranging from 120.9 to 343 nm and depths up to 2 microm have been achieved. This process offers excellent control over the nanopore size, aspect ratio and pitch of the fabricated nanostructures. The approach can also be extended to fabricate nanopore arrays of a wide range of materials.