Biodevices with engineered micro- and nanostructures are strongly needed for advancements in medical technology such as regenerative medicine, drug discovery, diagnostic reagents, and drug delivery to secure high quality of life. The authors produced functional biocompatible plastics and hydrogels with physical and chemical properties and surface microscopic shapes that can be freely controlled in three dimensions during the production process using the superior properties of quantum beams. Nanostructures on a biocompatible poly(L-lactic acid) surface were fabricated using a focused ion beam. Soft hydrogels based on polysaccharides were micro-fabricated using a focused proton beam. Gelatin hydrogels were fabricated using γ-rays and electron beam, and their microstructures and stiffnesses were controlled for biological applications. HeLa cells proliferated three-dimensionally on the radiation-crosslinked gelatin hydrogels and, furthermore, their shapes can be controlled by the micro-fabricated surface of the hydrogel. Long-lasting hydrophilic concave structures were fabricated on the surface of silicone by radiation-induced crosslinking and oxidation. The demonstrated advanced biodevices have potential applications in three-dimensional cell culture, gene expression control, stem cell differentiation induction/suppression, cell aggregation into arbitrary shapes, tissue culture, and individual diagnosis in the medical field.