A method and system increase processed specimen yield in the laser processing of target material that includes multiple specimens formed on a common substrate. Preferred embodiments implement a feature that enables storage in the laser processing system a list of defective specimens that have somehow been subject to error during laser processing. Once the common substrate has been completely processed, the system alerts an operator to the number of improperly processed specimens and gives the operator an opportunity to run a software routine, which in a preferred embodiment uses a laser to scribe a mark on the top surface of each improperly processed specimen.