Experimental modal analysis and testing of rotating machines imposes a significant complexity, compared to the approach for passive structures. In order to evaluate the applicability of modal analysis to rotors in operation, two commercially available algorithms were adapted to match with specific rotor behaviour. Both methods were validated by means of a numerical experiment. Then the modal analysis techniques were applied on a boilerfeed test pump with magnetic bearings. The diagnostic capabilities to detect increasing clearances were investigated. Additional knowledge of the rotor system allows to obtain some non-identifiable modal parameters or some system parameters. Finally a portable electromagnetic exciter was built; an experimental modal analysis was performed on a booster pump and on a boileerfeed pump in a thermal power plant.