During the last two decades we have witnessed tremendous advancement in the characterization and understanding of thermal transport in nanostructures, particularly in the ‘phonon boundary scattering’ regime where the characteristic size of nanostructures ranges from tens to hundreds nanometers and is comparable to phonon mean free path. This understanding is one of the key underlying reasons for improved performance observed in nanostructured thermoelectric materials. However, the boundary scattering mechanism may reach its limit and new mechanisms for improving thermoelectric performance need to be explored. One of the opportunities may arise from the study of thermal transport beyond the boundary scattering regime, where the characteristic size of nanostructures is below 10-20 nanometers and is comparable to phonon wavelength. However, there is little experimental work on thermal transport in nanostructures in this regime. In this talk, we will discuss our recent work on using rationally designed nanostructures to study nanoscale thermal and thermoelectric transport phenomena in this regime. We will describe the instrumentation we developed that enables the characterization of thermal and thermoelectric properties of these nanostructures and discuss and interpret the measurement results.