A system for generating and implementing programmed defects includes a lithography tool configured to form a multi-pattern structure including a first array pattern and a second array pattern on a sample. The first array pattern or the second array pattern contains a programmed defect to differentiate the first array pattern from the second array pattern. The system includes a metrology tool configured to acquire one or more images of the first array pattern and the second array pattern having a field-of-view containing the programmed defect. The system includes a controller including one or more processors. The one or more processors are configured to receive the images of the first array pattern and the second array pattern from the metrology, and determine a metrology parameter associated with the first array pattern or the second array pattern.
