A non-volatile memory is formed having shallow trench isolation structures between floating gates and having control gates extending between floating gates where shallow trench isolation dielectric is etched. Control of etch depth is achieved using ion implantation to create a layer of dielectric with a high etch rate compared with the underlying dielectric. A conductive layer overlies the substrate during implantation. A substrate having small polysilicon features in a memory array and large polysilicon features in a peripheral area is accurately planarized using protrusions in the peripheral area and a soft chemical mechanical polishing step that stops when protrusions are removed.