The present invention is related to a method and apparatus for cleaning a semiconductor substrate including on a surface of the substrate at least one structure comprising a first conducting or semiconducting material, surrounded by a layer of a second conducting or semiconducting material, said layer essentially extending over the totality of said surface, the first and second material being in physical contact, the method comprising the steps of: providing the substrate, positioning a counter-electrode facing the substrate surface, and supplying an electrolytic fluid to the space between the surface and the electrode, the counter-electrode acting as an anode in the galvanic cell defined by the substrate surface, the cleaning fluid and the counter-electrode.