Colloidal lithography is a popular, non-conventional process that uses two–dimensional self-assembled monolayer arrays of colloidal nanoparticles as masks for techniques such as etching or sputtering. Initiated Chemical Vapor Deposition (iCVD) is a surface controlled process which offers unprecedented opportunity for producing polymeric layers grafted to substrates with dangling vinyl bonds and patterned through a colloidal template. We demonstrate a generic “bottom-up” process as an inexpensive and simple technique for creating well-ordered arrays of functional patterned polymeric nanostructures. These patterns were produced from thin polymer films of p(butyl acrylate) and p(hydroxyethyl methacrylate), and are robustly tethered to the underlying substrate, as demonstrated by their ability to withstand aggressive solvents. Furthermore, using capillary force lithography, we created topographical templates for large-scale orientation of the nanoparticle assembly. Through this “top-down” approach, for assisting the bottom-up assembly, we present a process for multi-scale patterning of functional polymeric materials, without the need for expensive lithography tools.