Systems for assembling wafer stacks are provided. An embodiment of the system includes a vacuum chamber, a media deposition component and a wafer stack assembly component. The media deposition component is arranged within the vacuum chamber and is configured to deposit storage media upon a first wafer. The wafer stack assembly component also is arranged within the vacuum chamber. The wafer stack assembly component is configured to align the first wafer and a second wafer relative to each other and bond the first wafer and the second wafer together while at least a portion of the vacuum chamber is maintained under vacuum pressure. So configured, the interior chamber of the wafer stack can be formed as well as maintained under vacuum pressure. Methods also are provided.