Thermal management at solid interfaces presents a technological challenge for modern thermoelectric power generation. Here, we define a computational protocol to identify nanoscale structural features that can facilitate thermal transport in technologically important nanostructured materials. We consider the highly promising thermoelectric material, SrTiO3, where tilt grain boundaries lower thermal conductivity. The magnitude of the reduction is shown to depend on compositional and structural arrangements at the solid interface. Quantitative analysis indicates that layered nanostructures less than 10 nm will be required to significantly reduce the thermal conductivity below the bulk value, and it will be virtually independent of temperature for films less than 2 nm depending on the orientation with a reduction of thermal transport up to 75%. At the nanoscale, the vibrational response of nanostructures shows concerted vibrations between the grain boundary and inter-boundary regions. As the grain boundary acts markedly as a phonon quencher, we predict that any manipulation of nanostructures to further reduce thermal conductivity will be more beneficial if applied to the inter-boundary region. Our findings may be applied more widely to benefit other technological applications where efficient thermal transport is important.