[en] This work develops, discretizes, and validates a continuum model of a molybdenum disulfide (MoS2) monolayer interacting with a periodic holey silicon nitride (Si3N4) substrate via van der Waals (vdW) forces. The MoS2 layer is modeled as a geometrically nonlinear Kirchhoff–Love shell, and vdW forces are modeled by a Lennard-Jones (LJ) potential, simplified using approximations for a smooth substrate topography. Both the shell model and LJ interactions include novel extensions informed by close comparison with fully-atomistic calculations. The material parameters of the shell model are calibrated by comparing small-strain tensile and bending tests with atomistic simulations. This model is efficiently discretized using isogeometric analysis (IGA) for the shell structure and a pseudo-time continuation method for energy minimization. The IGA shell model is validated against fully-atomistic calculations for several benchmark problems with different substrate geometries. Agreement with atomistic results depends on geometric nonlinearity in some cases, but a simple isotropic St.Venant–Kirchhoff model is found to be sufficient to represent material behavior. We find that the IGA discretization of the continuum model has a much lower computational cost than atomistic simulations, and expect that it will enable efficient design space exploration in strain engineering applications. This is demonstrated by studying the dependence of strain and curvature in MoS2 over a holey substrate as a function of the hole spacing on scales inaccessible to atomistic calculations. The results show an unexpected qualitative change in the deformation pattern below a critical hole separation.