A three-dimensional semiconductor device, comprising: a programmable logic circuit constructed in a first module layer, said logic circuit input to output responses configurable to a user specification by configuring a plurality of control signals, each control signal received at a regulatory node in the logic circuit; and a configuration circuit constructed in a second module layer, said configuration circuit further comprising: a plurality of memory elements, each memory element having either one or two outputs, each memory element capable of storing one of two binary data values, each output coupled to one of said control signals, each control signal having either the same polarity of the stored memory bit or the opposite polarity of the stored memory bit; and a memory programming method to access each of said memory elements to alter the stored data value between said two binary data values to configure the control signals; wherein, the second module layer is positioned substantially above the first module layer in the semiconductor device.