The objective of this research is to develop an atomic force microscope based cyber-physical system that can enable automated, robust and efficient assembly of nanoscale components such as nanoparticles, carbon nanotubes, nanowires and DNAs into nanodevices. The approach in this project is based on the premise that automated, robust and efficient nanoassembly can be achieved through tip based pushing in an atomic force microscope with intermittent local scanning of nanoscale components. In particular, in order to resolve temporally and spatially continuous movement of nanoscale components under tip pushing, the research is exploring the combination of intermittent local scanning and interval non-uniform rational B-spline based isogeometric analysis in this research. Successful completion of this research is expected to lead to foundational theories and algorithmic infrastructures for effective integration of physical operations (pushing and scanning) and computation (planning and simulation) for robust, efficient and automated nanoassembly. The resulting theories and algorithms will also be applicable to a broader set of cyber physical systems. If successful, this research will lead to leap progress in nanoscale assembly, from prototype demonstration to large-scale manufacturing. Through its integrated research, education and outreach activities, this project is providing experiences and understanding in cyber-physical systems and nanoassembly for students from high schools to graduate schools. The goal is to increase interest in science and engineering among domestic students and therefore strengthen our competitiveness in the global workforce.