Methods are provided for manufacturing well-controlled, solid-state nanopores and arrays thereof. In one aspect, methods for manufacturing nanopores and arrays thereof exploit a physical seam. One or more etch pits are formed in a topside of a substrate and one or more trenches, which align with the one or more etch pits, are formed in a backside of the substrate. An opening is formed between the one or more etch pits and the one or more trenches. A dielectric material is then formed over the substrate to fill the opening. Contacts are then disposed on the topside and the backside of the substrate and a voltage is applied from the topside to the backside, or vice versa, through the dielectric material to form a nanopore. In another aspect, the nanopore is formed at or near the center of the opening at a seam, which is formed in the dielectric material.