A method of fabricating non-volatile memory is provided for memory cells employing a charge storage element with multiple charge storage regions. A first charge storage layer is formed over a tunnel dielectric layer at both a memory array region and an endpoint region of a semiconductor substrate. The first charge storage layer is removed from the endpoint region to expose the tunnel dielectric region. A second charge storage layer is formed over the first charge storage layer at the memory array region and over the tunnel dielectric layer at the endpoint region. When etching the second charge storage layer to form the stem regions of the memory cells, the tunnel dielectric layer provides a detectable endpoint signal to indicate that etching for the second charge storage layer is complete.