- Tremendous efforts have been directed at designing functional and well‐defined 3D structures in recent decades. Many approaches have been devised and are currently used to create 3D structures, including lithography, 3D printing, assembly, and template‐mediated (natural or synthetic) methods. Natural scaffolds offer some unique traits, as compared to their artificial counterparts, presenting highly ordered, porous, identical, abundant, and diverse structures. Various organisms, such as viruses, bacteria, diatoms, foraminifera, and others, are used as templates to form 3D structures. Herein, advancements made in using the shell of marine microorganisms, diatoms, and foraminifera, as scaffolds for designing functional 3D structures are reported. Furthermore, a succinct overview of various synthetic methods used to coat these scaffolds with inorganic materials (i.e., metals, metal oxides, and metal sulfides) is provided. Finally, the use of such fabricated functional 3D structures in a wide range of applications, such as catalysis, sensing, drug delivery, photo‐electrochemical uses, batteries, and others, is considered.