Fabricating semiconductor-based non-volatile memory that includes composite storage elements, such as those with first and second charge storage regions, can include etching more than one charge storage layer. To avoid inadvertent shorts between adjacent storage elements, a first charge storage layer for a plurality of non-volatile storage elements is formed into rows prior to depositing the second charge storage layer. Sacrificial features can be formed between the rows of the first charge storage layer that are adjacent in a column direction, before or after forming the rows of the first charge layer. After forming interleaving rows of the sacrificial features and the first charge storage layer, the second charge storage layer can be formed. The layers can then be etched into columns and the substrate etched to form isolation trenches between adjacent columns. The second charge storage layer can then be etched to form the second charge storage regions for the storage elements.