A method of processing a flash memory device provides a semiconductor substrate including a surface region and forming a gate dielectric layer overlying the surface region. The method forms a floating gate layer having a thickness and including a first floating gate structure overlying a first portion of the gate dielectric layer and a second floating gate structure overlying a second portion of the gate dielectric layer. The method forms a trench region interposed between the first and second floating gate structures and extending through the entire thickness and through a portion of the surface region into a depth of the substrate. The method fills the entire depth of the trench region in the substrate and a portion of the trench region over the substrate using a dielectric fill material. The method forms an oxide on nitride on oxide (ONO) layer overlying the first and second floating gate structures and the dielectric material and a control gate overlying the ONO layer.