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A new algorithm for estimating parameters of the fundamental component of a secondary current deformed due to CT saturation is presented in the paper. The algorithm is developed in an innovative 3D methodology where the samples of phase currents are considered as components of a 3D vector. The proposed algorithm can properly simultaneously remove the aperiodic components and distortions caused by CT saturation from a secondary current measured at the secondary side of CTs. Some results of simulation research has been provided and discussed.