In a method of patterning an integrated circuit, test layer thickness variation data is received when a test layer with a known thickness disposed over a test substrate undergoes tilted angle plasma etching. Overlay offset data per substrate locations caused by the tilted angle plasma etching is determined. The overlay offset data is determined based on the received thickness variation data. The overlay offset data is associated with an overlay between first circuit patterns of a first layer on the semiconductor substrate and corresponding second circuit patterns of a second layer disposed over the first layer on the substrate. A location of the substrate is adjusted based on the overlay offset data during a lithography operation to pattern a resist layer over the second layer. The second layer is patterned based on the projected layout patterns of the reticle and using the tilted angle plasma etching.