There is provided a system and method of segmenting an image of a fabricated semiconductor specimen. The method includes: obtaining a first probability map corresponding to the image representative of at least a portion of the fabricated semiconductor specimen and indicative of predicted probabilities of pixels in the image to correspond to one or more first structural elements presented in the image, obtaining a first label map informative of one or more segments representative of second structural elements and labels associated with the segments, performing simulation on the first label map to obtain a second probability map indicative of simulated probabilities of pixels in the first label map to correspond to the one or more segments, and generating a second label map based on the first probability map and the second probability map, the second label map being usable for segmentation of the image with enhanced repeatability.