The rotor is a key element of rotating machinery that can be used in different of mechanical devices such as gas turbines, industrial compressors, motors, and aero engines. The dynamic analysis of a rotor system with active magnetic bearings is presented in this paper. This system consists of a flexible shaft with a rigid disk and flexible bearings. An sys Workbench is used to study a 3D simulation of a finite element model. Correct estimation of the rotor's natural frequencies and mode shapes is required for rotating machinery safety procedures. In order to compute the natural frequencies and mode shapes of this system, in the first case it is assumed a free-free system in which no bearings are used, and the natural frequencies and mode shapes are calculated without rigid body modes. In the second case, the natural frequencies and mode shapes are determined with bearing stiffness. The natural frequencies are also evaluated using finite elements based on matlab code. A comparison between the two methods was carried out.