During the characterization by electron beam techniques including scanning electron microscope (SEM) and cathodoluminescence at low dimensions, some undesirable phenomena (unwanted effects) can be created, like the thermal effects (or electron beam damage), and these effects can damage the sample. This limits the information one can get from a sample or reduces image spatial resolution. In order to understand these effects, significant efforts have been made but these studies focused on the thermal properties, without a detailed study of the causes of nanoscale heating in the bulk of samples during the SEM-characterization. Additionally, it is very difficult to measure experimentally the heating because there are many variables that can affect the results, such as the current beam, accelerating energy, thermal conductivity and size of samples. Taking into account all the factors and in order to determine the local temperature rise during the electron beam characterization of AlGaN at low dimensions, we have used a hybrid model based on combined molecular dynamics and Monte Carlo calculation of inelastic interaction of electrons with matter to calculate the temperature elevation during the SEM-characterization which can be taken into account during the characterization of AlGaN at low dimension by electron beam techniques.