To address the need for the high precision synthesis of nanomaterials with the potential for high productivity, we present a novel design of a multi-step chemical vapor synthesis (CVS) reactor, which centers on the use of an atmospheric, continuous flow microplasma. Based on computational fluid dynamic gas flow simulations, the CVS reactor was designed to provide abrupt interaction steps to provide a well-defined and highly controlled start and stop to the nanomaterial (e.g., nanoparticle) growth. By applying this framework to gas-phase single-walled carbon nanotube (SWCNT) synthesis, the precise start and stop of the catalyst nanoparticle nucleation process can be done using the microplasma reactor (start) and carbon reactant gas to suppress further aggregation/promote SWCNT growth (stop), respectively. In so doing, we demonstrated the generation of controlled size of catalyst nanoparticles and SWCNTs despite high particle densities. We envision that our approach demonstrates the feasibility of fine structural control of nanomaterials through a multi-step CVS process with precisely regulating the aggregation time for high density particle flow, which overcomes the obstacle of both structural control and productivity.