The present disclosure provides an integrated circuit structure that includes a semiconductor substrate having a first region and a second region having an area less than about 10 micron×10 micron; a first material layer over the semiconductor substrate and patterned to have a first circuit feature in the first region and a first mark in the second region; and a second material layer over the first material layer and patterned to have a second circuit feature in the first region and a second mark in the second region. The first mark includes first mark features oriented in a first direction, and second mark features oriented in a second direction perpendicular to the first direction. The second mark includes third mark features oriented in the first direction, and fourth mark features oriented in the second direction.