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Modeling and simulating CO2 sequestration is a multi-disciplinary effort involving coupled physical and chemical phenomena. We present the challenges to generate 3D structural models that support multiphysics numerical simulations, specifically focusing on flow and poromechanics couplings. TotalEnergies, Stanford University and Lawrence Livermore National Laboratory are developing an open-source software called GEOS to run such simulation using a unique mesh. Beyond the need for meshes that are suited to several types of numerical methods, we need to use caution when determining the spatial extent of the modeled volumes. Here, poromechanical changes to stresses and deformations are not limited to reservoir layers where CO2 is stored but extend to surrounding formations. Modeling the reservoir and its surroundings is necessary to quantify fault reactivation, uplifting or caprock failure risks. We present the challenges of building 3D structural models and meshes suited to multiphysics simulations using implicit and explicit strategies. Finally, we present three types of mesh (tetrahedral, hex dominant and PEBI) that can be built on top of these structural models to run the poromechanics coupling with GEOS.