A method of forming a NAND flash memory includes anisotropically etching trenches of a gate stack down to an intermediate level in a floating gate polysilicon layer, leaving remaining portions of the floating gate polysilicon over the gate dielectric layer. Subsequently, forming a protective layer along exposed sides of the trenches. Then, electrically separating individual floating gates by a selective process that is directed to the remaining portions of the floating gate polysilicon layer exposed by trenches.