The essence of morphological design has been a fascinating scientific problem with regard to understanding biological mineralization. Particularly shaped amorphous silicas (plant opals) play an important role in the vital activity in rice plants. Although various organic matters are associated with silica accumulation, their detailed functions in the shape-controlled mineralization process have not been sufficiently clarified. In the present study, cellulose nanofibers (CNFs) were found to be essential as a scaffold for silica accumulation in rice husks and leaf blades. Prior to silicification, CNFs ~10 nm wide are sparsely stacked in a space between the epidermal cell wall and the cuticle layer. Silica nanoparticles 20–50 nm in diameter are then deposited in the framework of the CNFs. The shape-controlled plant opals are formed through the interfibrillar mineralization of silica nanoparticles on the CNF scaffold.