Scanning probe microscopy is widely known not only as a well-established research method but also as a set of techniques enabling precise surface modification. One such technique is local anodic oxidation (LAO). In this study, we investigate the LAO of MoSe2 transferred on an Au/Si substrate, focusing specifically on the dependence of the height and diameter of oxidized dots on the applied voltage and time of exposure at various humidities. Depending on the humidity, two different oxidation regimes were identified. The first, at a relative humidity (RH) of 60%-65%, leads to in-plane isotropic oxidation. For this regime, we analyze the dependence of the size of oxidized dots on the oxidation parameters and modify the classical equation of oxidation kinetics to account for the properties of MoSe2 and its oxide. In this regime, patterns with a maximum spatial resolution of 10 nm were formed on the MoSe2 surface. The second is the in-plane anisotropic oxidation regime that arises at a RH of 40%-50%. In this regime, oxidation leads to the formation of triangles oxidized inside the zigzag edges. Based on the mutual orientation of zigzag and armchair directions in successive oxidized layers, the stacking type and phase of MoSe2 flakes were determined. These results allow LAO to be considered not only as an ultra-high-resolution nanolithography method, but also as a method for investigating the crystal structure of materials with strong intrinsic anisotropy, such as transition metal dichalcogenides.