The tunable optoelectronic properties of stacked two-dimensional (2D) crystal monolayers are determined by their stacking orientation, order, and atomic registry. Atomic-resolution Z-contrast scanning transmission electron microscopy (AR-Z-STEM) and electron energy loss spectroscopy (EELS) can be used to determine the exact atomic registration between different layers, in few-layer 2D stacks; however, fast optical characterization techniques are essential for rapid development of the field. Here, using two- and three-layer MoSe<sub>2</sub> and WSe<sub>2</sub> crystals synthesized by chemical vapor deposition, we show that the generally unexplored low frequency (LF) Raman modes (<50 cm<sup>–1</sup>) that originate from interlayer vibrations can serve as fingerprints to characterize not only the number of layers, but also their stacking configurations. <i>Ab initio</i> calculations and group theory analysis corroborate the experimental assignments determined by AR-Z-STEM and show that the calculated LF mode fingerprints are related to the 2D crystal symmetries