A mechanical nanomanipulation system has been developed for the assembly and fabrication of nano-devices inside a scanning electron microscope (SEM). The mechanical manipulator is made up of commercially available actuators and positioning stages which consists of three individual operation units each having three linear stages and one rotational stage. Experiments were performed to construct 2D and 3D nanostructures with Au nanowires. Versatile manipulations including shape modification, length amendment, and connection of nanowires were carried out. An electron beam induced deposition (EBID) technique was used to grasp nano-materials and assemble them, enabling 2D and 3D manipulation to be easier to conduct. Experimental results show that this manipulator is possible to play an important role in enabling the technology of assembling nano-scale mechanical and electronic devices from prefabricated nano-scale components.