Molecular Nanotechnology (MNT) is nanotechnology using “molecular manufacturing”, an anticipated technology based on positionally-controlled mechanosynthesis guided by molecular machine systems. It involves combining physical principles demonstrated by chemistry, other nanotechnologies, and the molecular machinery of life with the systems engineering principles found in modern macroscale factories. Its most well-known exposition is in the books of K. Eric Drexler.

Ralph Merkle has compared today’s chemistry (in contrast to mechanosynthesis) to an attempt to build interesting Lego brick constructions while wearing boxing gloves. Because conventional chemistry has no tools that allow us to place a particular molecule in a particular place (so that it bonds in a predictable way), we must work with randomly moving molecules. As a result, when we cause a particular chemical reaction, we frequently get a mix of several different product species. We must often follow up after the reaction with a physical filtering process to extract the species we actually wanted, with the other species discarded as waste. Nanotechnology could therefore offer much cleaner manufacturing processes than today’s bulk technology offers.