A method to create an array of sub-5 nm nanogaps with self-aligned holes in a protective polymer overlayer is presented. The parallel formation of the nanogaps, intended for electrical sensing of biomolecules in an aqueous environment, is achieved by electromigration using a simple voltage ramp across parallel-connected electrode patterns with individual constrictions. It was observed that the nanogap always formed on the cathode side of a bowtie electrode, with corresponding hillocks on the anode side, with the distance of the gap/hillock formation from the constriction depending on the ambient temperature. This technique provides a practical means to fabricate a series of polymer-protected nanogaps with considerably higher efficiency than afforded by the normally slow serial process of electromigration.