Convection is the most important physical process that determines the structure of the envelopes of cool stars. It influences the surface radiation flux and the shape of observed spectral line profiles and is responsible for both generating and damping solar-like oscillations, among others. 3D numerical simulations of stellar surface convection have developed into a powerful tool to model and analyse the physical mechanisms operating at the surface of cool stars. This review discusses the main principles of 3D stellar atmospheres used for such applications. The requirements from stellar structure and evolution theory to use them as boundary conditions are analysed as well as the capabilities of using helio- and asteroseismology to reduce modelling uncertainties and probing the consistency and accuracy of 3D stellar atmospheres as part of this process. Simulations for the solar surface made by different teams are compared and some issues concerning the uncertainties of this modelling approach are discussed.