A method for transferring alignment marks between substrate systems includes providing a substrate having semiconductor devices and alignment marks in precise alignment with the semiconductor devices; and physically transferring and bonding the semiconductor devices and the alignment marks to a temporary substrate of a first substrate system. The method can also include physically transferring and bonding the semiconductor devices and the alignment marks to a mass transfer substrate of a second substrate system; and physically transferring and bonding the semiconductor devices and the alignment marks to a circuitry substrate of a third substrate system. A system for transferring alignment marks between substrate systems includes the substrate having the semiconductor devices and the alignment marks in precise alignment with the semiconductor devices. The system also includes the first substrate system, and can include the second substrate system and the third substrate system.