Autonomous capability in space systems is rapidly becoming a necessity for continued research and exploration. While these systems have traditionally behaved as passive observers, their remoteness and unique access to unexplored environments will likely result in future systems that behave more like active agents employed on our behalf. We may still determine the larger mission goals and priorities, but the systems themselves will be better able to direct their own movement, schedule, and operation. Autonomous control of computational hardware is one of the capabilities that is becoming more desirable. We describe and demonstrate the infrastructure necessary for a computing system to autonomously change its hardware while in operation, without requiring outside intervention. The system absorbs much of its complexity into itself, and assumes responsibility for its own resources and operation. This allows it to present a simpler interface to its environment, and to autonomously respond to changes within itself or its environment. Our demonstration system works internally with circuit netlists, that it dynamically parses, places, routes, configures, connects, and implements within itself-at the finest granularity available-while continuing to run. It models itself and its resource usage, and keeps the model tightly synchronized with the changes that it undergoes, to ensure proper behavior. The system is also able to dynamically avoid resources that have been reserved or masked out because of defects or damage.