We present an enhanced procedure to properly configure the simulation bounding box and discretization meshing scheme of a 3-D finite element full-wave EM simulator as applied to planar microwave circuits. Our procedure utilizes a meshing scheme that takes into account not only the wavelength at the highest simulated frequency, but also the geometrical objects associated to the simulated structure, as well as the expected physics behavior. We demonstrate how our physics-based meshing significantly improves the expected EM behavior of planar structures and decreases their sensitivity to the simulation bounding box, with respect to the conventional meshing scheme based on volumetric domains. We also show how a reasonable but inadequate meshing reduces the possibility of success when using direct optimization on the planar structure and makes the optimization process computationally more expensive. Our procedure is illustrated by a fifth order bandstop microstrip filter with L-shaped resonators simulated with COMSOL.ITESO, A.C.