Roll-to-roll freeze-drying (lyophilization) system and process for facilitating freeze-drying processes and enabling the collection of data by which a freeze-drying process can be monitored and evaluated. Such a system includes a roll-to-roll freeze-drying apparatus adapted to continuously freeze and dry a liquid to form a freeze-dried and encapsulate freeze-dried sheet portions of the freeze-dried sheet to create premeasured pouches containing the freeze-dried sheet portions. The system further includes a metrology section that monitors any of the freeze-dried sheet and the freeze-dried sheet portions during the freezing and drying of the liquid to generate data for controlling the freezing and drying of the liquid.