Transition metal dichalcogenides, a new class of layered materials, have recently been deemed as an excellent material platform for the further development of microelectronics. Contrary to the general trend, which is geared toward layers, we focus our attention on basic research regarding bulk PtSe2. The justification for this approach is based on the fact that some research (e.g., on the impact of the doping process on the material’s properties) can be performed on the bulk crystal. We believe that the conclusions drawn from our approximation can be extrapolated to thin films and monolayers. In this paper, we present a morphological study of the influence of the surface preparation procedure on the PtSe2 substrate. We show that mechanical exfoliation is one possible way to achieve a clean PtSe2 surface. However, STM measurements revealed that this process is insufficient to achieve an atomically clean surface. Subsequent additional annealing under UHV conditions led to an improved surface morphology by reducing the number of mobile PtSe2 flakes as well as the density of small surface clusters. Finally, STM measurements show other interesting surface structures, such as cracks, bulges, and flakes with heights lower than the apparent height typical of a PtSe2 monolayer.