Self-aligned trench filling to isolate active regions in high-density integrated circuits is provided. A deep, narrow trench is etched into a substrate between active regions. The trench is filled by growing a suitable dielectric such as silicon dioxide. The oxide grows from the substrate to fill the trench and into the substrate to provide an oxide of greater width and depth than the trench. Storage elements for a NAND type flash memory system, for example, can be fabricated by etching the substrate to form the trench after or as part of etching to form NAND string active areas. This can ensure alignment of the NAND string active areas between isolation trenches. Because the dielectric growth process is self-limiting, an open area resulting from the etching process can be maintained between the active areas. A subsequently formed inter-gate dielectric layer and control gate layer can fill the open area to provide sidewall coupling between control gates and floating gates.