This study deals with the preparation and characterization of metallic nanoinclusions on the surface of semiconducting Bi₂Se₃ that could be used for an enhancement of the efficiency of thermoelectric materials. We used Au forming a 1D alloy through diffusion (point nanoinclusion) and Mo forming thermodynamically stable layered MoSe₂ nanosheets through the reaction with the Bi₂Se₃. The Schottky barrier formed by the 1D and 2D nanoinclusions was characterized by means of atomic force microscopy (AFM). We used Kelvin probe force microscopy (KPFM) in ambient atmosphere at the nanoscale and compared the results to those of ultraviolet photoelectron spectroscopy (UPS) in UHV at the macroscale. The existence of the Schottky barrier was demonstrated at +120 meV for the Mo layer and −80 meV for the Au layer reflecting the formation of MoSe₂ and Au/Bi₂Se₃ alloy, respectively. The results of both methods (KPFM and UPS) were in good agreement. We revealed that long-time exposure (tens of seconds) to the electrical field leads to deep oxidation and the formation of perturbations greater than 1 µm in height, which hinder the I–V measurements.