Diatom frustules exhibit various sophisticated shapes with highly ordered hierarchical porous nanostructures, which are promising for applications in the biomimetic fabrication of nanostructured materials. We propose a universal biopattern transfer process for the fabrication of functional micro/nanostructures using diatom frustules as the biotemplates. Porous silicon microcylinders with a thickness of are fabricated by deep reactive ion etching of a silicon substrate, which is covered by a layer of diatom frustules. With a similar process, a fast atom beam technique is used to etch the silicon substrate and silicon nanolattices are obtained. By depositing a thin layer of gold film on the diatom bonded silicon substrate, followed by releasing the diatom frustules by diluted HF, gold nanodisks with a thickness of 30 nm are successfully fabricated. The nanodisk array arranges in diamond or radial patterns, replicating the nanostructure of diatom frustules. In addition, a parylene nanodot array is also demonstrated using this diatom-based biopattern transfer process.