The effect of rough structures on the electron emission under electron impact between 10 eV and 2 keV is investigated with a new version of the low energy electromagnetic model of GEANT4 (MicroElec). The inelastic scattering is modeled, thanks to the dielectric function theory and the Motts model of partial waves to describe the elastic scattering. Secondary electron emission is modeled for grooved and checkerboard patterns of different dimensions for aluminum and silver. The analyses are performed according to two shape parameters h/L and d/L, h being the height, L the width of the structures, and d the spacing between two neighboring structures. The secondary electron emission is demonstrated to decrease when h/L and d/L ratios increase. When the height reaches 10 times the lateral dimensions, the electron emission yield is divided by two compared to that of a flat sample. The optimization of the two aspect ratios leads to a reduction of the electron emission yield of 80% for grooved patterns and of 98% for checkerboard patterns. This purely geometric effect is similar for aluminum and silver materials. A simple analytical model, capable of reproducing the effect on the electron emission yield of checkerboard and grooved patterns, is proposed. This model is found to be in good agreement with the Monte Carlo simulations and some experimental measurements performed in our irradiation facility.