An integrated controller, logic circuit and memory array (“CLM”) semiconductor device includes stacked controller, memory array logic circuit and memory array wafers, or individual dies diced therefrom, which together operate as a single, integrated semiconductor flash memory device. The memory array logic circuit dies and/or the memory array dies may be formed with full-thickness plated or filled vias connecting to bond pads on opposed surfaces of the dies. The bond pads of the respective stacked semiconductor dies may be aligned and affixed to each other to electrically and mechanically couple each of the semiconductor dies in the respective wafers together.