Because most printed circuits are two-dimensional, the lithography technologies developed to manufacture them are also almost entirely planar fabrication technologies. In nanomanufacturing, however, there is also a need for three-dimensional fabrication, and this is accomplished by nanomachining.

Perhaps the most common form of nanomachining is done using scanning probe microscopes. However, research is being conducted into various other techniques, including the fabrication of structures by selectively growing carbon nanotubes, as well as the stretching of vaporized silicon.

The use of probes and other devices created through nanomachining to manipulate yet other nano-sized components to fabricate nanostructures is referred to as nanomanipulation.

Research is being carried out, for example, on the use of virtual reality technology-based holographic displays and pointers to boost precision and efficiency when manipulating atoms and molecules with an SPM probe. Molecular biomanipulation to sever or join DNA segments at desired locations is another area currently being developed.