Methods for pre-cleaning substrates having metal and dielectric surfaces are described. A substrate comprising a surface structure with a metal bottom, dielectric sidewalls, and a field of dielectric is exposed to a dual plasma treatment in a processing chamber to remove chemical residual and/or impurities from the metal bottom, the dielectric sidewalls, and/or the field of the dielectric and/or repair surface defects in the dielectric sidewalls and/or the field of the dielectric. The dual plasma treatment comprises a direct plasma and a remote plasma.