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A lid assembly is provided for covering and sealing a lyophilizer tray that contains a material for freeze-drying into a product in a lyophilizer chamber. The tray has an opening defined by a peripheral lip. The lid assembly includes a first lid disposable to seal around the lip of the tray, second lid disposed on the first lid, and a filter paper disposed therebetween. The first lid includes an opening. The second lid covers the opening and includes a hole over the opening. The filter paper is disposed over the opening between the first and second lids for inhibiting the product from escaping the tray through the hole while permitting water vapor to pass therethrough. With a lyophilization stopper to seal the hole, the tray containing the product can be protected from environmental humidity even after removal from the chamber.