This paper proposes the simulation of a complete mechanical model of a turbomolecular pump rotor, including rotor and blades flexibility, suspended by controlled active magnetic bearings. The mechanical model is composed of an eight stage blisk, attached to a shaft. Magnetic forces are linearized by first order Taylor expansion around a given point. Including blades and rotor flexibility makes the mechanical system asymmetric, so the equations of motion for the coupled system have periodic terms. A modal controller was designed to control rigid body modes, since the number of sensors is limited and no state observer is implemented. PID controllers are used for low frequency modes combined with second order filters to damp high frequency modes. First of all, stability analysis was carried out for the axisymmetric case. Secondly, blades flexibility was included. Forced response of the whole system to an impulsive force was studied. Divergent responses for the system in rotation were obtained as a second order filter pole possibly interacts with blades modes. Taking second order filters off the control loop allowed the system to be stable. These results show that the analysis method developed here is efficient to evaluate the performance of a controller in closed loop with the complete flexible system. This method may be used in industrial design processes as computation times for the complete system are very short.