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In this paper, a method for the fault section estimation that considers the network topology under the influence of a circuit breaker tripped by the previous fault is proposed. The proposed method uses a three-dimensional (3-D) matrix to represent the network topology and the protection systems. The proposed network matrix describes the sections that are protected by particular protective devices that can be changed according to the network topology. To deal with the uncertainties imposed on the protection systems, the fuzzy set theory was applied to the network matrix in order to examine the relationships between the operated protective devices and the fault section candidates. A systematic method for the fuzzy membership function for each relation is proposed. In the proposed method, the operated time sequences of the protective devices were employed because either the network matrix or the network topology varied whenever the operations of the circuit breakers occur. The efficiency and adaptivity of the proposed method were demonstrated in experimental studies on real power systems in the Korean electric power system, particularly in case of complicated multiple faults.