While various 3D printing technology has gained momentum in additive manufacturing, 3D nanoprinting remains challenging due to its requirement of high spatial precision. Combining scanning probe microscopy and nanolithography, microfluidic delivery, this presentation introduces a new chemistry means, known as “controlled assembly of molecules”, which enables 3D nanoprinting. While self-assembly of molecules is relatively well-known and frequently utilized in chemical synthesis and material science, controlled assembly of molecules represents a new concept and approach. The key to controlled assembly is the fact that ultra-small solution droplets exhibit different dynamics from those of larger ones. This new approach enables delivery of sub-femtoliter aqueous droplets containing designed molecules, which lead to well-defined features with dimensions as small as tens of nanometers, as illustrated in the Figure. The initial shape of the droplet and the concentration of solutes within the droplet dictate the final assembly of molecules due to the ultrafast evaporation rate and dynamic spatial confinement of the droplets. Applications of this technology in 3D nanoprinting are demonstrated. The level of control demonstrated in this work brings us closer to programmable synthesis for chemistry, as such benefit applications in materials science, additive manufacturing, and nanobiotechnology.