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Plasma polymerized nanoparticles (PPN) formed in plasma reactors have been considered undesirable in technological applications. More recently however, PPN were proposed as a new class of multifunctional nanocarriers for drug delivery. Therefore, synthesis of PPN requires cost-effective collection strategies that maximize yield and improve reproducibility. This work shows that the collection of PPN in dusty plasmas is modulated by modifying the geometry of substrates from planar to well-shaped collectors. The electric field profile around the wells acts as an electrostatic lens, concentrating nanoparticles and significantly bolstering process yield. The aggregation of PPN is governed by a balance between plasma expansion throughout the wells, inter-particle repulsion, particle size and density. PPN are readily dispersed in aqueous solution yielding monodisperse populations. The use of a disposable well-shape collector provides a cost-effective nanoparticle collection approach that can be adopted in a wide range of plasma polymerization configurations without the need for reactor re-design. Nanoparticle carriers are increasingly used for targeted drug delivery and other medical applications and ideally one would want several functionalities associated with one single nanocarrier. The authors report a method to improve collection and minimize aggregation of plasma polymerized nanoparticles by modifying the substrate design on which they are collected from a typical 2D geometry into a series of well-like structures which increase sample yield as well as inhibiting their fusion with the substrate itself.