A processing system for treating a substrate with a two-step process involving a chemical treatment of the exposed surfaces of the substrate by one or more process gasses in order to alter the surface chemistry of the substrate, and a post treatment of the exposed surfaces of the substrate in order to desorb the altered surface chemistry, the system comprising: a chemical treatment system for chemically altering exposed surface layers on said substrate comprising a temperature controlled chemical treatment chamber, a temperature controlled substrate holder mounted within said chemical treatment chamber and configured to be substantially thermally insulated from said chemical treatment chamber, a vacuum pumping system coupled to said chemical treatment chamber, and a gas distribution system configured to introduce one or more process gases into said chemical treatment chamber and having a temperature controlled portion exposed to said process gasses in said chemical treatment chamber; a thermal treatment system for thermally treating the substrate to desorb said chemically altered surface layers on said substrate, said thermal treatment system comprising a temperature controlled thermal treatment chamber, a temperature controlled substrate holder mounted within said thermal treatment chamber configured to be substantially thermally isolated from the thermal treatment chamber, and a vacuum pumping system coupled to said thermal treatment chamber; a controller coupled to said chemical treatment system and said thermal treatment system, and configured to set a chemical treatment chamber temperature, a chemical treatment gas distribution system temperature, a chemical treatment substrate holder temperature, a chemical treatment substrate temperature, a chemical treatment processing pressure, a chemical treatment gas flow rate, a thermal treatment chamber temperature, a thermal treatment substrate holder temperature, a thermal treatment substrate temperature, a thermal treatment processing pressure, and a thermal treatment gas flow rate; and, an isolation assembly disposed between said thermal treatment system and said chemical treatment system. a chemical treatment system for chemically altering exposed surface layers on said substrate comprising a temperature controlled chemical treatment chamber, a temperature controlled substrate holder mounted within said chemical treatment chamber and configured to be substantially thermally insulated from said chemical treatment chamber, a vacuum pumping system coupled to said chemical treatment chamber, and a gas distribution system configured to introduce one or more process gases into said chemical treatment chamber and having a temperature controlled portion exposed to said process gasses in said chemical treatment chamber; a thermal treatment system for thermally treating the substrate to desorb said chemically altered surface layers on said substrate, said thermal treatment system comprising a temperature controlled thermal treatment chamber, a temperature controlled substrate holder mounted within said thermal treatment chamber configured to be substantially thermally isolated from the thermal treatment chamber, and a vacuum pumping system coupled to said thermal treatment chamber; a controller coupled to said chemical treatment system and said thermal treatment system, and configured to set a chemical treatment chamber temperature, a chemical treatment gas distribution system temperature, a chemical treatment substrate holder temperature, a chemical treatment substrate temperature, a chemical treatment processing pressure, a chemical treatment gas flow rate, a thermal treatment chamber temperature, a thermal treatment substrate holder temperature, a thermal treatment substrate temperature, a thermal treatment processing pressure, and a thermal treatment gas flow rate; and, an isolation assembly disposed between said thermal treatment system and said chemical treatment system.