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Film bulk acoustic resonators (FBARs) are typically characterised by a network analyser on a probe station to extract the device parameters, which are then used for circuit design. These measured parameters are different from the intrinsic ones owing to the existence of parasitic effects from the pads and testing environment which may lead to failure of the designed circuits. A method is proposed to extract the intrinsic Q-factor and resonant frequencies of the FBARs from the measured S-parameters. Results show that the intrinsic series resonant frequency could be a few megahertz different from the measured one, and the intrinsic Q-factors could be up to 100% larger than the measured ones.