An improved apparatus and method for extracting pattern contour information from an inspection image in a multiple charged-particle beam inspection system are disclosed. An improved method for extracting pattern contour information from an inspection image comprises identifying, from an inspection image obtained from a charged-particle beam inspection system, a first pattern and a second pattern that partially overlap in the inspection image. The method also comprises generating a first separation image by removing an image area corresponding to the second pattern from the inspection image. The first separation image includes the first pattern of which a first part is removed when removing the image area corresponding to the second pattern. The method also comprises updating the first separation image to include image data representing the removed first part of the first pattern based on a first reference image corresponding to the first pattern.