The present invention relates to customizing individual workpieces, such as chip, flat panels or other electronic devices produced on substrates, by direct writing a custom pattern. Customization can be per device, per substrate, per batch or at some other small volume that makes it impractical to use a custom mask or mask set. In particular, it relates to customizing a latent image formed in a radiation sensitive layer over a substrate, merging standard and custom pattern data to form a custom pattern used to produce the customized latent image. A wide variety of substrates can benefit from the technology disclosed.