Nanostructuring of molecular monolayers is indispensable for integration of multiple functionality within a monolayer. Here, a fabrication method of two-component molecular assembly with nanoscale structures is demonstrated by a combination of reductive desorption of thiol molecules from a Au(111) substrate with local stabilization of the molecular layers using adsorption of Au nanoparticles. The average sizes of the obtained nanoscale molecular features were controlled by changing the size of nanoparticles. A unique functionality of size-controlled nanostructures was presented using redox responses of ferrocene-terminated molecules as a collective response of ferrocene moieties in each nanostructured assembly.