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A new approach to fabricating nanopore is presented. It is based on focused ion beam (FIB) sputtering to mill through a silicon nitride (Si3N4) membrane first, then followed by aluminum nitride (AlN) thin film deposition through the milled hole to narrow the pore size. FIB sputtering properties of Si3N4 membranes were investigated in order to achieve high aspect ratio holes through the membrane. The parameters of AlN deposition were optimized so that the final nanopore size can be finely controlled. A nanopore array with 70 nm pore-diameter was made in a Si3N4 membrane by FIB milling technology. The following AlN deposition was able to narrow the nanopores further down to 12 nm pore-diameter.