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We describe a hollow cathode plasma formed within a heated pocket deposition (HPD) source covered with a transparent conductive oxide (TCO)-coated substrate. Super-hydrophilic behavior and little change in TCO transmission of TCO substrates exposed to the plasma are observed. The “plasma cleaner” source was placed in-line with the CSU advanced deposition system (ARDS), and CdS and CdTe films were deposited on both plasma and conventionally cleaned substrates. Plasma-cleaned substrates result in improved cadmium sulfide films without pinholes after plasma exposure times as short as 5 sec. Cells formed with plasma cleaned substrates display improved VOC, fill factor, and efficiency.