The constructs of lipid molecules follow self-assembly, driven by intermolecular interactions, forming stacking of lipid bilayer films. Achieving designed geometry at nano- to micro-levels with packing deviating from the near-equilibrium structure is difficult to achieve due to the strong tendency of lipid molecules to self-assemble. Using ultrasmall (<fL) droplets containing designed molecules, our prior work has demonstrated that molecular assembly, in principle, is governed mainly by transient inter-molecular interactions under their dynamic spatial confinement, i.e., tri-phase boundaries during drying. As a result, the assemblies can deviate, sometimes significantly, from the near-equilibrium structures of self-assembly. The present work applies the approach and concept to lipid molecules using 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Taking advantage of the high spatial precision and the minute size of the delivery probe in our combined atomic force microscopy and microfluidic delivery, the transient shape of each liquid droplet is regulated. In doing so, the final geometry of the POPC assemblies has been regulated to the designed geometry with nanometer precision. The results extend the concept of controlled assembly of molecules to amphiphilic systems. The outcomes exhibit high potential in lipid-based biomaterial science and biodevice engineering.