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We investigated how density and quality of mesh around interest domain affect electromagnetic (EM) responses of 3D Earth layered media using finite element method (FEM). Effect of different mesh shapes was also investigated using a method of mixing structured and unstructured mesh. As a case study, we estimated the effects of meshing on selectivity phenomenon of seismic electric signal (SES). Our results suggest that the relative errors resulting from mesh effects may not be negligible, which may lead to some unconvincing explanation of the SES selectivity based on the numerical modeling results.