Ballistic electron emission microscopy (BEEM) has been used to study the processes affecting electron transport along the [0001] direction of finite layer MoS2 flakes deposited onto the surface of Au/Si(001) Schottky diodes. Prominent features present in the differential spectra from the MoS2 flakes are consistent with the density of states of finite layer MoS2 calculated using density functional theory. The ability to observe the electronic structure of the MoS2 appears to be due to the relatively smooth density of states of Si in this energy range and a substantial amount of elastic or quasi-elastic scattering along the MoS2/Au/Si(001) path. Demonstration of these measurements using BEEM suggests that this technique could potentially be used to study electron transport through van der Waals heterostructures, with applications in a number of electronic devices.