The layers largely aren't different. The end result is a vertical string of (theoretically identical) NAND memory cells filling the holes that were etched through the stack, with contacts at the top and bottom. At the edge of the stack, at the end of the fabrication process, they etch a staircase to expose one contact with each layer. See https://thememoryguy.com/3d-nand-how-do-you-access-the-contr...
How are the layers made different, without individual masking and etch?