Substrates for film deposition can be cleaned and/or modified in a variety of ways by various sputtering techniques, but this can be done controllably only by careful attention to all of the possible effects that can occur. In this review the known effects are summarised. Some of the system configurations that can be used are described. The physical and chemical sputtering effects are emphasised. These include rates of material removal and recontamination, backscattering, redeposition, trenching, faceting, cone formation, formation of altered surface layers, dissociation of compounds, diffusion, sublimation, ion implantation, crystallographic damage and radiation damage.