Sequence plays an important role in the self-assembly of 3D complex structures, especially for those with overlap, intersection, and asymmetry. Nevertheless, it is still difficult to program the sequence of self-determination, resulting in geometric and topological constraints. This paper demonstrates the nanoscale, programmable, self-assembly technique that uses electron irradiation as "hands" to manipulate the desired sequence of nanostructure movements. By assigning each assembly step to a specific task, the localized movement can be selected for the perfect time, which integrates the component accurately into the complex 3D structure without interrupting other parts of the assembly process. Peculiarities of localized movement, real-time monitoring, and surface patterns provide an opportunity for further innovation in nanotechnology, nanoscale test platforms, and advanced optical devices.