A method for fabricating a memory device with a self-aligned trap layer which is optimized for scaling is disclosed. In the present invention, a non-conformal film is deposited over the charge trapping layer to form a thick film on top of the core source/drain region and a pinch off and a void or a narrow channel at the top of the STI trench. An etch is performed on the non-conformal film to open pinch-off or widen the narrow channel in the non-conformal. The trapping layer is then completely or partially etched between the core cells. The non-conformal film is removed. And a top oxide is formed. The top oxide converts the remaining trap layer to oxide if the trapping layer is partially etched and thus isolate the trap layer.