With the growing interest in nanostructured materials, robust thermal engineering models are critical for thermal management in nanomaterials as well as the engineering of new materials with desired thermal properties. Thermal transport is often dominated by the scattering at interfaces rather than the bulk thermal conductivities of the constituent materials in structures where the characteristic length in at least one of the dimensions is on the order of tens of nanometers. There are mismatch models that have been developed to describe thermal transport at interfaces with some success. There are discrepancies between experimental measurements of thermal transport across interfaces and these models at room temperatures or higher. Recent efforts are being made to improve the modeling of nanostructured materials by using molecular dynamics techniques. The non-equilibrium molecular dynamics (NEMD) technique, which makes no assumptions of the scattering rules, is described with applications to thermal transport at single interfaces. The impact of interface imperfections due to lattice mismatches and interface mixing is determined for a fundamental case. Simulations indicate a linear relationship between thermal boundary conductance and temperature, which points towards the possible importance of inelastic scattering processes at the interface. The NEMD is extended to examine heat transfer in real nanostructured materials such as superlattices in attempts to develop suitable engineering models for thermal transport in such structures.