A lyophilization nest for preparing lyophilized substances, the nest comprising: a base comprising a bottom plate having a base edge extending upwardly from a perimeter thereof, the bottom plate having a top surface adapted to support a plurality of receptacles thereon, wherein the top surface of the bottom plate comprises one or more receptacle receiving portions formed therein, each of the receptacle receiving portions having features that conform to at least a bottom end of the receptacles to be received thereon and are constructed to conduct heat between the base and the receptacles supported thereon; a cover comprising a top plate having a cover edge extending downwardly from a perimeter thereof, the top plate having one or more vent holes extending therethrough; an interior space defined by the base and the cover when the base and the cover are in a closed relationship, the interior space being sized to accommodate the receptacles; a gasket situated between the base edge and the cover edge when the base and the cover are in the closed relationship, the gasket forming an air tight seal when compressed between the base edge and the cover edge; one or more sealing elements, each of the sealing elements being in closeable engagement with a corresponding one of the vent holes, such that the sealing elements and the corresponding vent holes are operable between: an open configuration in which the positions of the sealing elements relative to the corresponding vent holes permit fluid communication between the interior space and air external to the nest when the base and the cover are in the closed relationship; and a closed configuration in which the positions of the sealing elements relative to the corresponding vent holes do not permit fluid communication between the interior space and air external to the nest when the base and the cover are in the closed relationship, such that the interior space is sealed off to air external to the nest when the base and the cover are in the closed relationship. a base comprising a bottom plate having a base edge extending upwardly from a perimeter thereof, the bottom plate having a top surface adapted to support a plurality of receptacles thereon, wherein the top surface of the bottom plate comprises one or more receptacle receiving portions formed therein, each of the receptacle receiving portions having features that conform to at least a bottom end of the receptacles to be received thereon and are constructed to conduct heat between the base and the receptacles supported thereon; a cover comprising a top plate having a cover edge extending downwardly from a perimeter thereof, the top plate having one or more vent holes extending therethrough; an interior space defined by the base and the cover when the base and the cover are in a closed relationship, the interior space being sized to accommodate the receptacles; a gasket situated between the base edge and the cover edge when the base and the cover are in the closed relationship, the gasket forming an air tight seal when compressed between the base edge and the cover edge; one or more sealing elements, each of the sealing elements being in closeable engagement with a corresponding one of the vent holes, such that the sealing elements and the corresponding vent holes are operable between: an open configuration in which the positions of the sealing elements relative to the corresponding vent holes permit fluid communication between the interior space and air external to the nest when the base and the cover are in the closed relationship; and a closed configuration in which the positions of the sealing elements relative to the corresponding vent holes do not permit fluid communication between the interior space and air external to the nest when the base and the cover are in the closed relationship, such that the interior space is sealed off to air external to the nest when the base and the cover are in the closed relationship. an open configuration in which the positions of the sealing elements relative to the corresponding vent holes permit fluid communication between the interior space and air external to the nest when the base and the cover are in the closed relationship; and a closed configuration in which the positions of the sealing elements relative to the corresponding vent holes do not permit fluid communication between the interior space and air external to the nest when the base and the cover are in the closed relationship, such that the interior space is sealed off to air external to the nest when the base and the cover are in the closed relationship.