Methods, systems and devices for using charged particle beams (CPBs) to write different die-specific, non-volatile, electronically readable data to different dies on a substrate. CPBs can fully write die-specific data within the chip interconnect structure during the device fabrication process, at high resolution and within a small area, allowing one or multiple usefully-sized values to be securely written to service device functions. CPBs can write die-specific data in areas readable or unreadable through a (or any) communications bus. Die-specific data can be used for, e.g.: encryption keys; communications addresses; manufacturing information (including die identification numbers); random number generator improvements; or single, nested, or compartmentalized security codes. Die-specific data and locations for writing die-specific data can be kept in encrypted form when not being written to the substrate to conditionally or permanently prevent any knowledge of said data and locations.