A method of making a monolithic three dimensional NAND string, includes forming a stack of alternating layers of a first material and a second material different from the first material over a substrate, etching the stack to form at least one opening in the stack, forming a discrete charge storage material layer on a sidewall, forming a tunnel dielectric layer, forming a semiconductor channel material, selectively removing the second material layers without removing the first material layers, etching the discrete charge storage material layer to form a plurality of separate discrete charge storage segments, depositing an insulating material between the first material layers, selectively removing the first material layers to expose side wall of the discrete charge storage segments, forming a blocking dielectric, and forming control gates on the blocking dielectric.