The efficiency in modern technologies and green energy solutions has boiled down to a thermal engineering problem on the nanoscale. Due to the magnitudes of the thermal mean free paths approaching or overpassing typical length scales in nanomaterials (i.e., materials with length scales less than one micrometer), the thermal transport across interfaces can dictate the overall thermal resistance in nanosystems. However, the fundamental mechanisms driving these electron and phonon interactions at nanoscale interfaces are difficult to predict and control since the thermal boundary conductance across interfaces is intimately related to the characteristics of the interface (structure, bonding, geometry, etc.) in addition to the fundamental atomistic properties of the materials comprising the interface itself. In this paper, I review the recent experimental progress in understanding the interplay between interfacial properties on the atomic scale and thermal transport across solid interfaces. I focus this discussion specifically on the role of interfacial nanoscale “imperfections,” such as surface roughness, compositional disorder, atomic dislocations, or interfacial bonding. Each type of interfacial imperfection leads to different scattering mechanisms that can be used to control the thermal boundary conductance. This offers a unique avenue for controlling scattering and thermal transport in nanotechnology.