Several submicron probe technologies require the use of apertures to serve as electrical, optical or fluidic probes; for example, writing precisely using an atomic force microscope or near-field sensing of light reflecting from a biological surface. Controlling the size of such apertures below 100 nm is a challenge in fabrication. One way to accomplish this scale is to use high resolution tools such as deep UV or e-beam. However, these tools are wafer-scale and expensive, or only provide series fabrication. For this reason, in this study a versatile method adapted from conventional micromachining is investigated to fabricate protruding apertures on wafer-scale. This approach is called corner lithography and offers control of the size of the aperture with diameter less than 50 nm using a low-budget lithography tool. For example, by tuning the process parameters, an estimated mean size of 44.5 nm and an estimated standard deviation of 2.3 nm are found. The technique is demonstrated—based on a theoretical foundation including a statistical analysis—with the nanofabrication of apertures at the apexes of micromachined pyramids. Besides apertures, the technique enables the construction of wires, slits and dots into versatile three-dimensional structures.