This disclosure relates to a structure for aligning layers of an integrated circuit (IC) structure that may include a first dielectric layer positioned above a semiconductor substrate having one or more active devices, a trench stop layer positioned above the first dielectric layer, a second dielectric layer positioned above the trench stop layer, and a plurality of metal-filled marking trenches extending vertically through the second dielectric layer and the trench stop layer and at least partially into the first dielectric layer. The metal-filled trenches are electrically isolated from any active devices contained in the IC.