A freeze dryer processes aseptic bulk powder products. The freeze dryer freezes the product by mixing an atomized spray of product with sterile liquid nitrogen to produce a frozen powder. The frozen powder is freeze dried in a vessel by dielectrically heating the frozen powder using electromagnetic radiation such as microwave radiation or infrared radiation, and the frozen powder is continuously agitated using a sterilizable apparatus such as a series of vibrating shelves to maintain even heating and to prevent agglomeration.