Exploration of the bioinspired silicification of artificial scaffolds is crucial to understanding and engineering the hierarchically complex and elaborate three-dimensional (3D) frustules of diatoms, which have high porosity and mechanical stability with related gas diffusion and storage properties. Herein, we report on the bioinspired silicification of the nanostructured surfaces of hexagonally close-packed silica bead (hc-SB) arrays using a liquid-phase deposition (LPD) method. This process, governed by the kinetics of silicification, was controlled using the concentration of the reactants and the reaction temperature and monitored in real time using a quartz-crystal microbalance, which allowed the investigation of the silicification on the surface during the LPD reaction. These heterogeneous LPD reactions on hc-SB arrays were optimized to mimic natural 3D hierarchical structures. Anisotropic silicification of the nanostructures occurred owing to differences in the energy and local concentration of silicic acid on the nanostructured surface. A 3D hierarchical pore network was realized via a heterogeneous LPD reaction by controlling the size, location, and arrangement of the SBs. We believe that our silicification process on nanostructured surfaces can lead to great improvements in the bioinspired morphogenesis-based engineering of 3D hierarchical structures.