Lyophilization systems and methods

System and methods related to lyophilization of pharmaceutical products are disclosed. In some embodiments, vials of product are moved through a system using one or more movers which are electromagnetically levitated and moved through the system without making mechanical contact with each other or the system. Load lock chambers may allow a mover to enter from one process region's environment and then be brought to an environment condition of the next process region to allow materials to be passed through conditioning, nucleation, and/or vacuum drying regions prior to finally exit the system to an unloading zone. The movers may then be cleaned or reloaded with vials to begin the process again with a new load of vials.