Nanopatterns have applications in many areas including sensors, optoelectronics, and crystallization screening. Particle lithography is a convenient method to manufacture nanoring nanopatterns based on organosilane surface chemistry. The pattern thickness is generally limited to the monolayer thickness. This work is focused on the chemical vapor deposition conditions that yield nanopatterns with multilayer thickness. The supra-monolayer n-octadecyltrichlorosilane (OTS) nanoring patterns are made using polystyrene particle lithography. The supra-monolayer nanopatterns are used as "nano-flasks" to deposit and nucleate nanoparticles of small organic molecules including n-docosane, aspirin, and clarithromycin. The supra-monolayer OTS nanopattern is an effective template for nanoparticle array deposition of all three chemicals with high degree of fidelity to the substrate pattern. The nanoparticle size is varied by solution concentration. The preferential deposition of the organic molecules inside the nanoring is attributed to the dewetting of the liquid film on the nanopattern. The dewetting process effectively distributes the liquid film among the "nano-flasks" so that millions of solution experiments can be carried out in isolated droplets with droplet volume as small as 1×10(-10) nL. The research demonstrates a method to manufacture "nano-flask" arrays for high-throughput nanoparticle deposition trials and manufacture of monodisperse organic/drug nanoparticles through self-assembly.