Preceded by unbalance, misalignment is the second major mechanical fault in rotating machine applications. In spite of using modern alignment techniques like laser alignment tool, the accidental misalignment arises over a period of continuous operation due to many reasons. This can lead to excessive forces on components of rotating systems, which ultimately greatly influence on its vibration spectrum. The study presents the results of Harmonic analysis of the Aluminum (Al) shaft rotor bearing system with rigid coupling, under parallel misalignment, using FEA. It show-cases vibration spectrum due to the misalignment. The results are compared with experimental results based on FFT analyzer for different sub critical speeds. Misalignment effect at coupling location is simulated using nodal force vector. The force vector is found using coupling stiffness matrix, derived from geometrical and material properties and instantaneous parallel misalignment between the two coupled shafts. Based on the FEA and experimental results, parallel misalignment in the shaft rotor system can be predicted almost at all speeds by observing 2X characteristics frequency of operating speed. However to diagnose the nature of misalignment, the knowledge of natural frequency of the system plays a crucial role. It facilitates determination of other dominant characteristic frequencies. An FEA approach is proposed for the first time for determination of magnitude and harmonic nature of the misalignment excitation of the system with rigid coupling