A method of combinatorial masking employs a combinatorial etch mask that includes a top layer of a stack of material layers and a secondary mask on the top layer to etch other material layers of the stack. The method includes patterning a first layer at a top of the stack of material layers, and providing the secondary mask on top of the patterned first layer. The method further includes etching other material layers of the stack including a second layer below the first layer with the combinatorial mask and then etching the first layer along with the other material layers of the stack excluding the second layer using the secondary mask as an etch mask.