A metrology design and verification framework is provided, which includes methods and systems for metrology structure identification in an integrated circuit design data block, design rule checking, hierarchal design of metrology target structures to minimize random errors, and metrology design rule verification of metrology target design files. In-die metrology targets are identified using various filtering methods and/or designed as hierarchical structure within dies or outside the dies. Particularly, metrology target design files are generated, which are hierarchical in structure and compatible with design rule checks. Design rule check takes into account the hierarchical and often repetitive target designs in the verification process. Layouts may be verified using design rule checks at different levels of design rules, which may be combined to remove rule violations and errors prior to actual target production.