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This paper presents a model predictive control strategy for a three-level flying capacitor converter with output LC filter for UPS applications. In order to reduce the calculation effort (64 different switching possibilities for one prediction step) in a first step the best one of the 19 voltage vectors is determined. After that the best switching state which delivers this voltage vector is determined regarding the flying capacitor voltage balancing and the switching effort, making use of a hysteresis-based algorithm. A disturbance observer is used to estimate the output currents of the LC filter which are normally not measured. The proposed principle can be easily extended to flying capacitor converters with more than three voltage levels.