Many new fabrication technologies, from nanotechnology and MEMS to printed organic semiconductors, center on constructing arrays of large numbers of sensors, actuators, or other devices on a single substrate. The utility of such an array could be greatly enhanced if each device could be managed by a programmable controller and all of these controllers could coordinate their actions as a massively-parallel computer. Kentucky Architecture nanocontroller array with very low per controller circuit complexity can provide efficient control of nanotechnology devices. This thesis provides a detailed description of the control hierarchy of a digital system needed to build "nanocontrollers" suitable for controlling millions of devices on a single chip. A Verilog design and FPGA prototype of a nanocontroller system is provided to meet the constraints associated with a massively-parallel programmable controller system.