Abstract: Issues of boundary discretization of the boundary element method and effective measures to enhance the computational accuracy and numerical stability are investigated for the extraction of capacitance matrices of complex microfine wires. The influences of open boundary size, open boundary discretization, conductor discretization on the computational accuracy, as well as the issues of pseudo-solutions and matrix singularity are analyzed. A two-stage automatic iterative boundary element method (AIBEM) based on the conductor discretization iteration and the open boundary iteration is proposed. Two methods for generating coefficient matrices for multilayer media issue, namely the full-domain method and the regional decomposition method, are described by means of examples. The investigation results show that the coefficient matrices generated in the boundary loop suffer from the problem of error equalization and coordination, so for complex models it is essential to choose elaborately the numbers of discrete elements for each of the line segments as well as the dimensions of the open boundary, howerver using AIBEM can provide economic discretization parameters, which can effectively avoid matrix singularity and improve the convergence stability. The computational results are compared with those from finite-element method, analytical method, transmission line method and method of moment, which confirmed the reliability of the proposed algorithm.