Laser ablation in conjunction with Raman spectroscopy can be used to attain a controllable reduction of the thickness of exfoliated black phosphorus flakes and simultaneous measurement of the local temperature. However, this approach can be affected by several parameters, such as the thickness-dependent heat dissipation. Optical, thermal, and mechanical effects in the flakes and the substrate can influence the laser ablation and may become a source of artifacts on the measurement of the local temperature. In this work, we carry out a systematic investigation of the laser thinning of black phosphorus flakes on SiO2/Si substrates. The counterintuitive results from Raman thermometry are analyzed and elucidated with the help of numerical solutions of the problem, laying the groundwork for a controlled thinning process of this material.