In order to continue the progress of nanotechnology in producing effective and efficient mechanical, electrical, and optical nanostructure devices, the physics of the devices in micro and nanoscale need to be understood and accurately modeled. For instance, the demand for high areal density data storage devices such as hard disk drives (HDDs) has led to heat-assisted magnetic recording (HAMR) and microwave-assisted magnetic recording (MAMR) technologies. These technologies require layered nanostructures with thicknesses of a few nanometers and a high temperature difference across the layers. These technologies introduce thermo-mechanical design challenges since the nanoscale heat transfer mechanics do not follow the classical heat transfer theories. In this work, the mechanisms of heat transfer in the nanoscale are studied.A typical nanostructure is composed of several conductive and thin insulating layers (a few microns to a few nanometers) with a temperature difference between the layers where some insulating layers maintain the temperature gradient in such small spacings. In these structures, the dominant heat transfer mechanisms are radiation due to high temperature gradient and phonon conduction due to thin conductive layers. First, we review the fundamentals of electromagnetism and lattice vibrations and derive the classical heat transfer theories, and discuss the assumptions that lead to them. We show that the classical theories do not consider the wave nature of the heat transfer mechanisms (heat carriers) and are derived based on equilibrium thermodynamics. These assumptions make the obtained results inapplicable to our problems. Next, we study the recent theories and methods used to solve steady-state nanoscale heat transfer problems, and we further develop more accurate models of calculations.In this work, we study the mechanisms of heat transfer in nanostructures and present simulations for the thermal analysis of various multilayered structures. We show how the radiative and phonon conduction heat fluxes across a nanoscale vacuum gap vary as a function of the gap spacing, and focus on the problems with large heat flux across nanostructures. Next, we consider the effect of the interference of the heat carriers, due to their wave nature, on radiation and phonon conduction. The heat transfer coefficient (HTC) for various structures used in the current HDD technology is characterized by different temperature differences and conditions. The presented results are also used in collaboration with other researchers in simulations of HDI of HAMR HDDs.Next, the presented algorithms are used to simulate radiation in multilayered structures with absorbing materials, where the speed of propagation for absorbing materials is based on a recent model in literature that predicts the depth-dependent speed of electromagnet waves inside materials. We also present a novel way to describe the distribution of the thermal emission inside a multilayered structure using one distribution function instead of using multiple distributions for layers with different temperatures, which we call the unified field. This model is more accurate than the models in the preceding chapters at predicting the HTC for the phonon conduction in materials under some conditions