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Fast algorithms are developed in this work for solving the system matrix resulting from a frequency-domain layered finite element based analysis of integrated circuits. The frequency-domain layered finite element method represents a 3-D layered system by a 2-D layered system, and further by a single-layered one. The reduced system matrix is generally denser than the original sparse matrix. In this paper, we show that 1) the dense matrix-vector multiplication can be performed in linear complexity; in addition, the reduction cost can be bypassed, 2) an effective preconditioner can be developed to converge the iterative solution of the reduced system matrix in a small number of iterations, and 3) the preconditioner can be solved in linear complexity. As a result, the reduced system matrix can be solved efficiently. The algorithms are rigorous without making any approximation. They apply to any arbitrarily-shaped multilayer structure. Numerical results demonstrated the accuracy, effectiveness, and efficiency of the proposed algorithms in analyzing on-chip circuits.