Recent advances in biomedicine largely rely on the development in nanoengineering. As the access to unique properties in biomaterials is not readily available from traditional techniques, the nanoengineering becomes an effective approach for research and development, by which the performance as well as the functionalities of biomaterials has been greatly improved and enriched. This review focuses on the main materials used in biomedicine, including metallic materials, polymers, and nanocomposites, as well as the major applications of nanoengineering in developing biomedical treatments and techniques. Research that provides an in-depth understanding of material properties and efficient enhancement of material performance using molecular dynamics simulations from the nanoengineering perspective are discussed. The advanced techniques which facilitate nanoengineering in biomedical applications are also presented to inspire further improvement in the future. Furthermore, the potential challenges of nanoengineering in biomedicine are evaluated by summarizing concerned issues and possible solutions.