The self-polymerization of 4-chloromethylphenyltrichlorosilane (CMPS) was studied within spatially confined nanoholes on Si(111) using atomic force microscopy (AFM). Surface platforms of nanoholes were fabricated within a film of octadecyltrichlorosilane using immersion particle lithography. A heating step was developed to temporarily solder the silica mesospheres to the surface, to enable sustained immersion of mesoparticle masks in solvent solutions for the particle lithography protocol. Substrates with a film of mesospheres were heated briefly to anneal the particles to the surface, followed by a rinsing step with sonication to remove the silica beads to generate nanopores within an octadecyltrichlorosilane (OTS) film. Nanopatterned surface templates were immersed in CMPS solutions and removed at different time points to monitor the successive growth of nanostructures over time. Analysis of AFM images after progressive exposure of the nanoholes to solutions of CMPS provided quantitative information and details of the surface self-assembly reaction. Pillar nanostructures of CMPS with different heights and diatmeters were produced exclusively within the exposed areas of the substrates. Throughout the reaction, the surrounding matrix of OTS-passivated substrate did not evidence growth of CMPS; the surface assembly of CMPS was strictly confined within the nanopores. The diameter of the CMPS nanostructures grew to match the initial sizes of the confined areas of Si(111) but did not nanopores. The diameter of ther CMPS nanostructures grews to match the initial sizes of the confined areas of Si(111) but did not spread out beyond the edges of the OTS nanocontainers. However, the vertical growth of columns was affected by the initial size of the sites of uncovered substrate, evidencing a direct correspondence; larger sites produced taller structures, and correspondingly the growth of shorter structures was observed within smaller nanoholes. The heights of CMPS nanostructures indicate that multilayers were formed, with taller columns generated after longer immersion times. These experiments offer intriguing possibilities for using particle lithography as a general approach for nanoscale studies of molecular self-assembly.