Systems and methods for protecting biological or other material from contamination through the steps of filling, freeze-drying, packaging, storing and use are disclosed. A system can include a flexible container, at least two membranes configured to transmit air or solvent vapor out of the flexible container, and a port to allow for the introduction or withdrawal of a material or substance into or out of the flexible container. The system can optionally further comprise a membrane frame supporting at least one of the membranes and engaged with at least one column member. The at least one column member can be configured to maintain the membranes and the membrane frame a spaced distance from one or more materials received within the flexible container. Upon application of a downward force, the at least one column member can assume a collapsed configuration. A method can include inserting a biological material into a flexible container, freeze-drying the biological material, moving the freeze-dried biological material to a portion of the flexible container that includes at least one port, and sealing the biological material within the portion.
