Indeed that both electrode will be sputterred. However, the electric field
that is applied to the electrode surface is different. I am not quite sure
about the exact relation of this but basically the larger the electrode
area, the smaller the applied electric field, so that the energy of the
ions that bombard the surface would be lower. Usually in a RF sputtering
system, the target will be one electrode while the sample connected with
the whole chamber served as the counter electrode, so that the sputtering
effect to the sample surface is minimized.
Better grab a book about sputtering, there it is usually explained
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