Nanostructured plasmonic metamaterials, including optical nanoantenna arrays, are important for advanced optical sensing and imaging applications including surface-enhanced fluorescence, chemiluminescence, and Raman scattering. Although designs typically use ideally smooth geometries, realistic nanoantennas have nonzero roughness, which typically results in a modified enhancement factor that should be involved in their design. Herein we aim to treat roughness by introducing a realistic roughened geometry into the finite element (FE) model. Even if the roughness does not result in significant loss, it does result in a spectral shift and inhomogeneous broadening of the resonance, which could be critical when fitting the FE simulations of plasmonic nanoantennas to experiments. Moreover, the proposed approach could be applied to any model, whether mechanical, acoustic, electromagnetic, thermal, etc, in order to simulate a given roughness-generated physical phenomenon.