A multilevel semiconductor device, the device including: a first level including a first array of first programmable cells and a first control line; a second level including a second array of second programmable cells and a second control line; and a third level including a third array of third programmable cells and a third control line, where the second level overlays the first level, where the third level overlays the second level, where the first programmable cells are self-aligned to the second programmable cells, and where a programmable logic cell includes a plurality of the first programmable cells and a plurality of the second programmable cells.