Measurements of the electron transparency of a Micromegas mesh are compared to simulations. The flux conservation argument is shown to lead to inaccurate estimates of the transparency, the importance of accurate geometric modelling of the mesh is discussed and the effect of the dipole moment of the mesh is demonstrated. This study provides a validation of the microscopic simulation methods specifically developed for micropattern devices where the characteristic dimensions are of the same order of magnitude as the electron mean free path in the gas.