A method of forming an NVM cell and a logic transistor uses a semiconductor substrate. A metal select gate of the NVM cell is formed over a high-k dielectric as is metal logic gate of a logic transistor. The logic transistor is formed, including forming source/drains, while the metal select gate of the NVM cell is formed. The logic transistor is protected while the NVM cell is then formed including forming a charge storage region using metal nanocrystals and a metal control gate over a portion of the metal select gate and a portion of the charge storage region over the substrate. The charge storage region is etched to be aligned to the metal control gate.