New micro- and nanoscale devices require electrically isolating materials with specific thermal properties. One option to characterize these thermal properties is the atomic force microscopy (AFM)-based scanning thermal microscopy (SThM) technique. It enables qualitative mapping of local thermal conductivities of ultrathin films. To fully understand and correctly interpret the results of practical SThM measurements, it is essential to have detailed knowledge about the heat transfer process between the probe and the sample. However, little can be found in the literature so far. Therefore, this work focuses on theoretical SThM studies of ultrathin films with anisotropic thermal properties such as hexagonal boron nitride (h-BN) and compares the results with a bulk silicon (Si) sample. Energy fluxes from the probe to the sample between 0.6 µW and 126.8 µW are found for different cases with a tip radius of approximately 300 nm. A present thermal interface resistance (TIR) between bulk Si and ultrathin h-BN on top can fully suppress a further heat penetration. The time until heat propagation within the sample is stationary is found to be below 1 µs, which may justify higher tip velocities in practical SThM investigations of up to 20 µms−1. It is also demonstrated that there is almost no influence of convection and radiation, whereas a possible TIR between probe and sample must be considered.