In this paper, current research work on the development of an automated nano handling station in a scanning electron microscope (SEM) is presented. An experimental setup is described, in which two mobile microrobots cooperate in the vacuum chamber of an SEM. The robots are positioned by a closed-loop controller with sensor data, which is provided by three charge-coupled device cameras and the SEM. Continuous pose estimation is carried out by processing noisy SEM images in real time. To enable the automation of complex tasks, a client-server control system that can integrate various microrobots and sensors is introduced. Finally, the overall system is evaluated by automatic handling of transmission electron microscope lamellae.