The system is used for manufacturing, portioning and packaging biotechnological active pharmaceutical substances. The operations of weighing the substance matter, preparing the recipe, treating the plugs, sterilisation of the portioning tanks, bottling the medicament, freeze-drying it, sealing bordering and visual inspection are combined fully automated in this sterile system. Moreover, the complete handling of the frames (container pallets) including the transfer and magazining, cleaning and sterilisation is integrated fully automated in the system.