The invention provides methods of using positionally controlled molecular tools in an inert environment (such as ultra high vacuum) to fabricate complex atomically precise structures, including diamond, graphite, nanotubes, fullerenes, additional sets of the selfsame molecular tools, and others. Molecular tools have atomically precise tooltips which interact directly with a workpiece to add, remove, and modify specific atoms and groups of atoms, and have handles by which they can be held and positioned; tools can be recharged after use. Specific tooltips are brought into contact with and bond to specific feedstock molecules distributed on a presentation surface, and then transfer said feedstock molecules to specific atomic sites on a workpiece using mechanosynthetic chemical reactions. Specific sites on a workpiece can be made chemically reactive, facilitating the transfer of specific groups to them. Repeated applications of molecular tools at different locations on a workpiece can build a desired atomically precise structure.