The nanometer-scale control of the structures of silica films achieved in biomimetic silicification processes by simple counteranion exchange of q-PDMAEMA was demonstrated. A uniform PDMAEMA film was generated on gold, and the PDMAEMA film was subsequently quaternized with bromo-ethane. Biomimetic silicification was performed on each substrate at room temperature and was confirmed by Fourier-transform infrared (FT-IR) spectroscopy. The tightly associated polymeric films would be more impermeable to silicic-acid derivatives, which results in the formation of smaller silica nanoparticulates. The counteranions were found to significantly affect the morphogenesis of silica nanoparticulates on surfaces by interacting with and shaping q-PDMAEMA films differently based on their charge density. The biomimetic approach would be one possible method for controlling inorganic structures on surfaces under mild conditions at the nanometer scale.