Contour-based array inspection of patterned defects

A system for detecting defects in an array on a substrate, the system comprising:

• a source for generating an incident electron beam;
• a scanning system for controllably deflecting the incident electron beam to scan the incident electron beam over a target region on the substrate such that secondary electrons are emitted therefrom;
• a detection system for detecting the secondary electrons and generating an image data frame of the target region;
• and
• a control and processing system with control code programmed to
• generate a reference image using a cell image that was previously determined to be defect free,
• generate a reference contour image which includes contours of the reference image, and
• use the reference contour image to detect defects in the array of cells on the substrate.