During operation, the mating surfaces of a metal-to-metal seal typically undergo significant plastic deformation, which in turn can have beneficial effect on its performance. In previous studies, it has, for instance, been shown that plastic deformation can provide for better sealing during unloading. Those studies did, however, only consider flow through unrealistically small domains. Therefore, it is possible that this might be a size effect, which would not be apparent in a real situation with a much larger domain. In this paper, we develop a model which can handle real-sized seal domains at the same time as fine details of the surface topography. More precisely, we construct a two-scale model, in which the global scale represents the seal domain and where the influence of the fine details at the local scale are represented by a stochastic element. By means of this stochastic two-scale model, we show that the beneficial effect associated with the plastic deformation persists also when real-sized seal domains are considered.