With rising science contents of the engineering research and education, we give examples of the quest for fundamental understanding of heat transfer at the atomic level. These include transport as well as interactions (energy conversion) involving phonon, electron, fluid particle, and photon (or electromagnetic wave). Examples are 1. development of MD and DSMC fluid simulations as tools in nanoscale and microscale thermophysical engineering. 2. nanoscale thermal radiation, where the characteristic structural size becomes comparable to or smaller than the radiation (electromagnetic) wavelength. 3. laser-based nanoprocessing, where the surface topography, texture, etc., are modified with nanometer lateral feature definition using pulsed laser beams and confining optical energy by coupling to near-field scanning optical microscopes. 4. photon-electron-phonon couplings in laser cooling of solids, where the thermal vibrational energy (phonon) is removed by the anti-Stokes fluorescence; i.e., the photons emitted by an optical material have a mean energy higher than that of the absorbed photons.Nanoscale and Microscale Thermophysical Engineering, 12: 1-60, 2008 Copyright Ó Taylor 5. exploring the limits of thermal transport in nanostructured materials using spectrally dependent phonon scattering and vibrational spectra mismatching, to impede a particular phonon bands.These examples suggest that the atomic-level heat transfer builds on and expands electromagnetism (EM), atomic-molecular-optical physics, and condensed-matter physics. The theoretical treatments include ab initio calculations, molecular dynamics simulations, Boltzmann transport theory, and near-field EM thermal emission prediction. Experimental methods include near-field microscopy.Heat transfer physics describes the kinetics of storage, transport, and transformation of microscale energy carriers (phonon, electron, fluid particle, and photon). Sensible heat is stored in the thermal motion of atoms in various phases of matter. The atomic energy states and their populations are described by the classical and the quantum statistical mechanics (partition function and combinatoric energy distribution probabilities). Transport of thermal energy by the microscale carriers is based on their particle, quasi-particle, and wave descriptions; their diffusion, flow, and propagation; and their scattering and transformation encountered as they travel. The mechanisms of energy transitions among these energy carriers, and their rates (kinetics), are governed by the match of their energies, their interaction probabilities, and the various hindering-mechanism rate (kinetics) limits. Conservation of energy describes the interplay among energy storage, transport, and conversion, from the atomic to the continuum scales.With advances in micro-and nanotechnology, heat transfer engineering of micro-and nanostructured systems has offered new opportunities for research and education. New journals, including Nanoscale and Microscale Thermophysical Engineering, have allowed communi...