The purpose of this paper is to present a novel approach to study sliding friction by the use of 3D multiscale coupling techniques. We highlight the difficulties of using multiscale schemes that couple molecular dynamics (MD) with finite elements to perform sliding contact between rough surfaces. The paper is comprised of systematic comparisons between the coupled model with an equivalent MD domain as well as reduced models. Reduced models appear inadequate for reproducing the time evolution of frictional forces as the small depths yield a stiffening of the contact region. The overlap domain used in the multiscale scheme is successful at capturing the complex deformation dynamics beneath the surface. Yet our results call for further developments in multiscale coupling strategies to allow a more rigorous treatment of heat exchanges through the overlap region.