A method of forming a capped die forms a cap wafer having a top side and a bottom side. The bottom side is formed with 1) a plurality of device cavities having a first depth, and 2) a plurality of second cavities that each have a greater depth than the first depth. At least some of the plurality of second cavities each generally circumscribe at least one of the device cavities. The method then secures the cap wafer to a device wafer in a manner that causes a plurality of the device cavities each to circumscribe at least one of circuitry and structure on the device wafer. Next, the method removes at least a portion of the top side of the cap wafer to expose the second cavities. This forms a plurality of caps that each protect the noted circuitry and structure.