VaryVac, a robotically-controlled vacuum nest for filter plates used in DNA prep, protein purification, solid-phase separations and other microplate-based filtration, combines automated lid opening and sealing with closed-loop control of programmable vacuum levels. An on-board computer that controls and monitors vacuum ramp-up, hold level, and ramp down. It can be set to notify the user if a desired threshold vacuum level is not obtained, such as from a damaged plate rim or other causes of an incomplete vacuum seal. It enables users to completely avoid wasted or incomplete vacuum operations. It can be loaded and operated manually, but is also compatible with robot loading systems from most manufacturers.