Abstract: A sample treatment system for automated extraction of compounds is disclosed. The system includes a housing defining an enclosure including a top cover having an open ended well for allowing a sample plate to nest therein, a automated shuttle means for lateral transportation and vertical lifting of both a waste and a collection plate to selectively address an area below the sample plate for the through passage of fluid from the sample plate and a digitally controlled variable speed vacuum pump operatively coupled to said housing for evacuating air from the enclosure to a degree below atmospheric pressure for through passage of fluid from the sample plate to either the waste plate or collection plate. The shuttle means includes motor drives and positive position feedback for precisely laterally and vertically positioning both the waste and collection plates.