A novel numerical de-embedding scheme called the short-open calibration (SOC) technique, in conjunction with the vector finite element method (FEM), has been developed to characterize two-port network of arbitrarily shaped, three-dimensional discontinuities in microwave circuits. This SOC technique is effectively implemented into the FEM for boundary truncation of the unbounded circuit structures. In such a manner, fast convergence of iterative solver for large-sparse linear matrix equations from FEM is achieved. The SOC technique is used to remove parasitic effects brought by the approximation of the impressed voltage source and also the problem of resulting consistency between the two-and threedimensional simulations. Scattering parameters of discontinuous sections are constructed from the definition of port voltages and currents. Numerical solutions are well compared with those published in the available literatures. It is demonstrated that the features of the SOC technique are advantageous when combined with FEM for electromagnetic problems.