The present invention relates to a system and method for providing real-time visual feedback to automatically control actions of multiple autonomous nano-robots with manipulators in order to perform specific nano-manipulation or nano-assembly tasks. In the system and method of the present invention, the visual feedback is obtained for the nano-manipulators and the nano-components via an electronic microscopy system. The system of the present invention comprises essentially at least one slave Scanning Electron Microscope (SEM) with imaging system deployed with autonomous manipulators inside, and a master controller system with Graphical User Interface (GUI). In the system of the present invention, said slave SEM provides real-time vision feedback for the sensed environment for said master controller, and said master controller provides real-time feedback control command for the required task to said slave SEM.