A plasma processing module for processing a substrate includes a plasma containment chamber having a feed gas inlet port capable of allowing a feed gas to enter the plasma containment chamber of the plasma processing module during the processing of the substrate. An inductively coupled source is used to energize the feed gas and striking a plasma within the plasma containment chamber. The specific configuration of the inductively coupled source causes the plasma to be formed such that the plasma includes a primary dissociation zone within the plasma containment chamber. A secondary chamber is separated from the plasma containment chamber by a plasma containment plate. The secondary chamber includes a chuck and an exhaust port. The chuck is configured to support the substrate during the processing of the substrate and the exhaust port is connected to the secondary chamber such that the exhaust port allows gases to be removed from the secondary chamber during the processing of the substrate. A chamber interconnecting port interconnects the plasma containment chamber and the secondary chamber. The chamber interconnecting port allows gases from the plasma containment chamber to flow into the secondary chamber during the processing of the substrate. The chamber interconnecting port is positioned between the plasma containment chamber and the secondary chamber such that, when the substrate is positioned on the chuck in the secondary chamber, there is no substantial direct line-of-sight exposure of the substrate to the primary dissociation zone of the plasma formed within the plasma containment chamber.