A method of fabricating a semiconductor structure includes forming a thermal oxide layer, a polysilicon layer and a first dielectric layer on a substrate and using a mask to form at least one opening therein. Dielectric spacers are then formed in the opening and a trench having a self-aligned reduction in width due to the dielectric spacers is etched into the substrate beneath the opening. A dielectric trench liner is then formed prior to filling the trench with polysilicon. A second mask is then used to form isolation element openings in the first dielectric layer in which shallow isolation elements are formed.