Spherical and hexagonal CaCO₃ with hierarchical structures were prepared on surfactant-modified PET substrate between the interfaces of saturated Ca(OH)₂ solution and n-hexane. The results show that CaCO₃ synthesis follows the same nanoparticle-mediated self-organization process but the morphology of the products strongly depends on the properties of surfactant modification. The synthetic procedure offers several important characteristics for CaCO₃ superstructure fabrication. Surfactants in this experimental system act not only as templates, but also as regulators for the fabrication of superstructures. This biomimetic system will be promising in synthesizing other functional nanoparticles or nanodevices.