A method of making a semiconductor structure uses a substrate having a background doping of a first type. A gate structure has a gate dielectric on the substrate and a select gate layer on the gate dielectric. Implanting is performed into a first portion of the substrate adjacent to a first end with dopants of a second type. The implanting is prior to any dopants being implanted into the background doping of the first portion which becomes a first doped region of the second type. An NVM gate structure has a select gate, a storage layer having a first portion over the first doped region, and a control gate over the storage layer. Implanting at a non-vertical angle with dopants of the first type forms a deep doped region under the select gate. Implanting with dopants of the second type forms a source/drain extension.