Structuring materials is one mechanism to influence the thermal conductivity and thus thermoelectric efficiency. In order to investigate the scattering of phonons in multilayer structures we developed a beam matching technique, which is based on the concept of individual phonons and their scattering at interfaces. One of the major goals is to efficiently determine the complex band structure of the bulk materials. The complex band structure is determined using selected k‐points on a triangulated grid in the complex plane of wave vectors perpendicular to the interface. Matching the phonon modes at an interface is translated to a singular value problem. Its null‐vectors provide the coupling coefficients of the phonon modes across the interface. Besides giving explicit access to the modes as they scatter at the interface, the technique provides the transfer matrices, that provide the transmission coefficient of any multilayer structure. The transmission coefficient, in turn, yields the phononic thermal conductance for coherent transport. The knowledge of the matched phonons forms the basis of investigating incoherent transport under the influence of phonon–phonon or impurity scattering.