This methodology has been selected for the cover page of a Special Issue on Phase Change and Ovonic Materials in Physica Status Solidi Rapid Research Letters (https://doi.org/10.1002/pssr.202170014). In this work, layered Ge2Sb2Te5 films were grown by solid source molecular beam epitaxy on Sb-passivated Si(111) surfaces with a control down to a single lamella. By means of Raman spectroscopy, a non-destructive characterization tool, the evolution of the peak positions with film thickness was investigated. This unveils the unexplored low frequency region, namely the in-plane Eg and out-of-plane A1g modes between 30 and 40 cm-1, which mostly modulate the interactions across the van der Waals gap and not those inside the lamella. Calculations based on density functional theory allow a clear identification of the experimental Raman peaks, confirming the trends observed experimentally. Similar dependencies of the Raman peaks are shown also for Ge1Sb2Te4 obtained in turn by post-growth annealing of the epitaxial GeSbTe series. In contrast to transmission electron microscopy techniques, which requires cumbersome preparation and statistical analysis, the method is quick and robust and highlights the advantages of the molecular beam technique for the precise control of the layer size and the importance of the vibrational modes for probing the 2D nature of the material.