The atom manipulation technique based on scanning tunneling microscope refers to a method of relocating single atoms or molecules on a certain surface at atomic accuracy by using an atomically sharp tip, which is a unique and powerful tool for studying the quantum physics and prototype quantum devices on a nanometer scale. This technique allows us to build artificial structure atom-by-atom, thus some desired interesting quantum structures which are difficult to grow or fabricate by conventional methods could be realized, and unique quantum states, spin order, band structure could be created by the fine tuning of the structural parameters like lattice constant, symmetry, periodicity, etc. Combined with nanosecond scale time domain electric measurement and autonomous control technique, the atom manipulation would be useful in exploring the atomic precision prototype quantum devices, and providing some valuable knowledge for future electronics. In this review, we introduce the atom manipulation technique and related milestone research achievements and latest progress of artificial quantum structures, including electronic lattices with exotic quantum states on Cu(111), quantum dots on III-V semiconductors, magnetic structures with tunable spin order, structures for quantum information storage and processing, prototype Boolean logic devices and single atom devices. The STM lithography and autonomous atom manipulation are discussed as well. With such improvements, this technique would play more important roles in developing the functional quantum devices in future.