A semiconductor wafer processing system including a factory interface operating at atmospheric pressure and mounting plural wafer cassettes and plural wafer processing chambers connected to the factory interface through respective slit valves. A robot in the factory interface can transfer wafers between the cassettes and the processing chambers. At least one of the processing chambers can operate at reduced pressure The processing chamber may be a rapid thermal processing chamber including an array of lamps irradiating a processing volume through a window. The lamphead is vacuum pumped to a pressure approximating that in the processing volume. A multi-step process may be performed with different pressures. The invention also includes a wafer access port of a thermal processing chamber which can flow an inert gas in outside of the slit valve to thereby form a gas curtain outside of the opened slit to prevent the out flow of toxic processing gases.