A method of making a semiconductor device on a semiconductor substrate, comprising: forming a first oxide layer on the semiconductor substrate for use as a gate dielectric for a high voltage transistor in a first region of the semiconductor substrate and in a second region of the semiconductor substrate surrounded by an isolation region; performing decoupled plasma nitridation to the first oxide layer to form a nitrogen-rich oxide layer on a the complete top surface of the first oxide layer, wherein the nitrogen-rich oxide layer has a nitrogen concentration of not more than 10 atomic percent and a thickness of not more than 1 nm; forming a first well region in said second region of the substrate inside said isolation region by implanting dopants into said second region through the first oxide layer and the nitrogen-rich oxide layer; performing a patterned etch of the first oxide layer and the nitrogen-rich oxide layer over the first well region wherein the etch is aligned to the isolation region so as to expose said first well region; after performing the patterned etch, forming a second oxide layer on the first well region for use as a gate dielectric for a non-volatile memory transistor in and over the first well region; forming a charge storage layer (28, 30) including nanocrystals and a 15nm thick oxide layer above and around said nanocrystals on the nitrogen-rich oxide layer and on the second oxide layer; and removing the charge storage layer (28, 30) including the nanocrystals on the nitrogen-rich oxide layer using hydrofluoric acid that is selective between the charge storage layer (28, 30) including the nanocrystals and the nitrogen-rich oxide layer so that the nitrogen-rich oxide layer functions as an etch stop layer and leaving the charge storage layer (28, 30) on the second oxide layer. forming a first oxide layer on the semiconductor substrate for use as a gate dielectric for a high voltage transistor in a first region of the semiconductor substrate and in a second region of the semiconductor substrate surrounded by an isolation region; performing decoupled plasma nitridation to the first oxide layer to form a nitrogen-rich oxide layer on a the complete top surface of the first oxide layer, wherein the nitrogen-rich oxide layer has a nitrogen concentration of not more than 10 atomic percent and a thickness of not more than 1 nm; forming a first well region in said second region of the substrate inside said isolation region by implanting dopants into said second region through the first oxide layer and the nitrogen-rich oxide layer; performing a patterned etch of the first oxide layer and the nitrogen-rich oxide layer over the first well region wherein the etch is aligned to the isolation region so as to expose said first well region; after performing the patterned etch, forming a second oxide layer on the first well region for use as a gate dielectric for a non-volatile memory transistor in and over the first well region; forming a charge storage layer (28, 30) including nanocrystals and a 15nm thick oxide layer above and around said nanocrystals on the nitrogen-rich oxide layer and on the second oxide layer; and removing the charge storage layer (28, 30) including the nanocrystals on the nitrogen-rich oxide layer using hydrofluoric acid that is selective between the charge storage layer (28, 30) including the nanocrystals and the nitrogen-rich oxide layer so that the nitrogen-rich oxide layer functions as an etch stop layer and leaving the charge storage layer (28, 30) on the second oxide layer.