Over the last decade, scanning probe microscopy (SPM), including scanning tunneling microscopy (STM) and atomic force microscopy (AFM), has become a powerful manipulation technique by virtue of its ability to interact with individual adsorbed nanoparticles with nanoscale precision on the surface. In this article, the principles, procedures and applications of both STM and AFM-based technologies for manipulation of atoms, molecules, and nanoclusters are reviewed with an emphasis on their ability to create a wide variety of nanostructures. In the manipulation of single atoms and molecules, the interaction among the atoms/molecules, surface, and tip are specifically discussed first. The approach for positioning the atom/molecule from and to the desired locations and precisely controlling its movement is also elaborated for each specific manipulation technique. The applications of these techniques for fabricating different nanostructures and nanosystems are then presented. In the manipulation of nanoclusters, different nanocluster-substrate pairs in different environments with their potential applications in electronics, biology, and medicine are specifically evaluated. Finally, concluding remarks are provided, where the scopes for technological improvement and future research are recommended.