An apparatus for atomic scale processing is provided. The apparatus may include a reactor (100) and an inductively coupled plasma source (10). The reactor may have inner (154) and outer surfaces (152) such that a portion of the inner surfaces define an internal volume (156) of the reactor. The internal volume of the reactor may contain a fixture assembly (158) to support a substrate (118) wherein the partial pressure of each background impurity within the internal volume may be below 10−6 Torr to reduce the role of said impurities in surface reactions during atomic scale processing.