There are provided a method of inspecting the inspection area and an inspection system thereof. The inspection system comprises an inspection control unit operatively coupled to an inspection tool unit and to a recipe generating unit. The inspection control unit is configured to obtain the design data and the inspection recipe; to provide local segmentation of at least one inspection PoI comprised in an inspection image captured from the inspection area by the inspection tool unit, thereby obtaining inspection structural elements comprised in the at least one inspection PoI, the local segmentation is provided using segmentation configuration data specified in the inspection recipe; to identify one or more target structural elements and design structural elements corresponding thereto, identifying is provided using design association data specified in the inspection recipe; and to enable metrology measurements for the one or more target structural elements using the identified design structural elements.