There are provided system and method of performing metrology operations related to a specimen. The method comprises: generating an examination recipe in accordance with a metrology application, the examination recipe specifying one or more metrology objects and one or more metrology operations related to the metrology application; obtaining an image-based representation of the specimen and a design-based representation of the specimen; mapping between the design-based representation of at least first metrology object and the image-based representation of at least first metrology object; and performing at least first metrology operation of the one or more metrology operations according to the examination recipe using the mapping, the at least first metrology operation specified as related to the at least first metrology object and to be performed on at least the image-based representation of the specimen.