Recent developments of wide bandgap devices using AlGaN thin films have opened discussions about this ternary alloy’s fabrication methods. The growth of GaN-based thin films on silicon and sapphire wafers still presents a challenge due to the nitrides’ high lattice mismatch with the single-crystalline structures of the substrates. Until AlGaN bulk wafers at a reasonable price are commercially available, the coatings by chemical vapor depositions or physical vapor depositions are the best options to fabricate layers for the thickness of half a micron. In this paper, the deposition from a target using an RF magnetron system is studied to fabricate AlGaN thin films at room temperature (25°C) and high temperature (700°C). The accomplished vital aspects are the nucleation transition of the layers with fewer impurities, the formation of wurtzite crystal structures, the analysis of the deposited compound’s basic configuration and the observation of the surface topography. A study of the elemental and surface characterization is conducted to measure nitride treatment’s impact after the fabrication of AlGaN thin films on silicon and sapphire. It is observed that 50% of the compound is nitrogen and the other 50% is evenly divided between aluminium and gallium. Moreover, it is shown that with 10 h of deposition at room temperature, the formation of a wurtzite crystal structure is improved as the count continued to increase and the crystalline structure of AlGaN can be obtained if a correlation is maintained in the process parameters.