In this paper, a numerical short-open calibration (SOC) technique is presented to numerically model and de-embed a variety of non-planar periodic guided-wave structures based on the 3-D full-wave finite element method (FEM). A simple current source or lumped-port model is introduced in formulation of a determinant FEM algorithm. By incorporating the SOC in the FEM solver, the intrinsic port discontinuity caused by this port model is then fully removed or calibrated out of the core non-planar periodic guided-wave structure during the calibration process. Because of the 3-D nature of FEM, the effective per-unit-length parameters of the core periodic guided-wave structure, i.e., effective propagation constant and effective characteristic impedance, are extracted successfully. Two numerical examples, including microstrip line with periodical loading of shorting pins and metal-insulator-metal composite right/left handed structure, are numerically modeled for demonstration and verification. Extracted results have validated the feasibility and accuracy of the presented FEM-SOC, thereby exhibiting its advanced capability in numerical modeling and de-embedding of non-planar structures with complicated configurations.