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This paper describes the key components that need to be developed, implemented and integrated in order to make full automation on the nano-scale possible. Multiple nanohandling robots are integrated into a flexible robot cell that can quickly adapt to different manipulation scenarios. An approach for the physical actuation of the employed smart actuators is given. A real-time capable control architecture makes efficient and reliable automation possible. With specialized methods of collision avoidance and path planning, the actual automation sequences can then abstract from the complex task of motion planning for individual robots. Furthermore, the major challenges when performing calibration and adjustment on the nanoscale are highlighted.