Nanotechnology has been used extensively in the past decade in a variety of research fields including renewable energy, manufacturing systems, and biomedical engineering, to name a few. In biomedical engineering, the nanoscale sizes and large ratios of surface area to its volume of the developed nanostructures can confer remarkable physical or physiological properties to facilitate chemical, biological, and thermal interactions with cells and molecules in biological tissue. As a result, nanostructures have great potential as carriers of therapeutic agents, contrast agents in bio-imaging, and strong thermal energy generators or absorbers. Improved control over nanostructure size, shape, and surface coating allows rapid research advancements in diagnosis, imaging, and treatment for various diseases. However, there are also challenges when working at this size-scale. Targeted delivery of nanoparticles, controlled therapeutic agent release from nanoparticles into tissue, distributions of nanostructure-related thermal energy deposition for tissue damage, etc., are transport phenomena that are especially relevant for nanotherapeutics and contrast agents. These considerations require multiscale and/or multiphysical modeling and in vivo or in vitro experiments using living and biological systems.