A storage system for storing samples, such as frozen biological samples in RFID-tagged vials. The storage system has a plurality of lowest-level containers, such as sample boxes; a plurality of mid-level containers, such as shelves and racks; and a highest-level container, such as a mechanical freezer. Each lowest-level container receives a plurality of samples in a corresponding plurality of storage locations, each mid-level container receives two or more lowest-level containers, and the highest-level container receives the two or more mid-level containers. Each mid-level container and each lowest-level container has a corresponding indicator device. A controller sub-system tracks the locations of samples stored in the storage system. When a desired sample is to be retrieved from the storage system, the controller sub-system activates (a) the indicator device corresponding to the mid-level container containing the desired sample and (b) the indicator device corresponding to the lowest-level container containing the desired sample.