Molecular nanotechnology is the future capability to design and build systems to atomic precisions. This paper motivates the desire of molecular nanotechnology for space exploration with a review of potential benefits, and reviews relevant progress to date for molecular nanotechnology. It provides a framework of challenges that need to be resolved before molecular nanotechnology can be applied to space systems, with discussion on addressing those challenges. The primary focus is in the area of developing tools for automated design of molecular components, using molecular connector components as an example, and in developing tools for generating reaction pathways to fabricate molecular components that can integrate with tools for developing molecular components. The secondary focus is issues for the molecular fabrication system, including integration with the design of end product space systems.