Microwave vacuum drying is getting more and more popular—thanks to its known advantageous features. In spite of its uniqueness, there is a rightful resistance and mistrust because of the nonhomogeneous electric field that may cause nonhomogeneous temperature distribution in the workload. In practice the best uniformity of power density and the shortest drying time are sought simultaneously, thus the drying method is close to its secure limit. Control and monitoring of a running process remains unsolved but even experimental mapping is rather circuitous. The dielectric and thermal properties of a complex pharmaceutical composition are rarely known, and moreover, they change during a drying process, which makes accurate mathematical modelling rather uncertain. For that very reason preliminary tests can never be neglected. The aim of our study is to experimentally map and evaluate the heat distribution quantitatively. To get a 3D overview of a free-flowing bulk, the workload was divided with Teflon layers to form cross-sectional surfaces. After dissipation of microwave energy, IR thermocartograms were taken and the temperature distribution was evaluated quantitatively. The “3D layered thermography” method offers reliable and workload-specific information, via a simple executable technique, for optimization of a microwave assisted drying process.