A self-aligned nanolithography approach is reported to form a nanoscale via hole in a nanogap. Field emission between two opposite electrodes of a nanogap is used to expose the polymer resist within the nanogap region. A via hole pattern forms in the nanogap area after the exposure process. The via hole pattern is obtained by ablating the polymer resists within the nanogap between two nanoelectrodes upon applying a certain bias voltage. The diameter of the via holes can be controlled to have comparable dimension to the nanogap width. Single or array of via holes have been demonstrated with variable diameters from 20 nm to over 100 nm. The self-aligned via nanoholes can be used to deposit functional nanostructures that are precisely aligned with the nanogap electrodes to form electrode-nanoisland-electrode tunneling junction devices. Electrical characterization of such devices shows typical tunneling characteristics at room temperature. These studies demonstrate a general pathway to making electrical contacts to individual nanostructures for functional nanodevice engineering.