A key feature of single-cell marine organisms called diatoms is their silica exoskeleton with nanoporous morphology. These naturally grown structures provide a promising basis for new biomimetic structural designs, but may also be used directly in their native form. Microscale diaphragms found in nature often can withstand large deformations. They also show vibration eigenfrequencies in the high MHz to GHz range. These structural properties open up the possibilities for the development of production technologies based on micromanipulation of bio-inspired or bio-derived microscale structures. In this work we report the results of FEM simulations aimed at investigating the effects of stiffness, pore diameter, and thickness on the vibrational characteristics of diatom frustule structures.