A method of making a semiconductor device includes a substrate having a semiconductor layer having a first portion for non-volatile memory and a second portion exclusive of the first portion. A first dielectric layer is formed on the semiconductor layer. A plasma nitridation is performed on the first dielectric layer. A first plurality of nanoclusters is formed over the first portion and a second plurality of nanoclusters over the second portion. The second plurality of nanoclusters is removed. A second dielectric layer is formed over the semiconductor layer. A conductive layer is formed over the second dielectric layer.