There have been enormous interests in mimicking biological system, which often possess remarkable optical, structural and mechanical properties. Nature's control over biomineralization processes involves an intimate interaction with macromolecules, both as structured organic matrices and as soluble additives, resulting in hierarchical organization ranging from the nanometer to macroscopic length scales. Guided by these biological principles, we investigate the combination of bottom-up and top-down approaches to control the synthesis of inorganic materials, including silica nanoparticles and calcium carbonate single crystals, on micropatterned, functional organic templates, and understand the specific interactions at the organic-inorganic interface. In a separate vein, we demonstrate a novel method for DNA-based, directional assembly of PEG-ylated rod-shaped nanoparticles, which are created by holographic lithography with precise size, shape and aspect ratios.