Systems and methods for designing and manufacturing customized prefabricated buildings in optimized modules. In one embodiment, a system for manufacturing a customized prefabricated building includes a computer-usable medium having a sequence of instructions which, when executed by a processor, causes said processor to execute a process including receiving a specification for a customized prefabricated building that identifies components for the prefabricated building and the dimensions of the components, modularizing the specification into modules meeting overall length, width, and height limitations, and optimizing the modularization; a programmable manufacturing system controller coupled to the computer-usable medium and configured to generate instructions for manufacturing the said optimized modules having the plurality of components identified in the specification received by the computer-usable medium; and a manufacturing system coupled to the programmable manufacturing controller configured to execute the instructions generated by the programmable manufacturing controller for building the said optimized modules having the specified plurality of components.