The present application discloses methods, systems and devices for using charged particle beam tools to pattern and inspect a substrate. The inventors have discovered that it is highly advantageous to use write and inspection tools that share the same or substantially the same stage and the same or substantially the same designs for respective arrays of multiple charged particle beam columns, and that access the same design layout database to target and pattern or inspect features. By using design-matched charged particle beam tools, correlation of defectivity is preserved between inspection imaging and the design layout database. As a result, image-based defect identification and maskless design correction, of random and systematic errors, can be performed directly in the design layout database, enabling a fast yield ramp.