Various embodiments include computer-implemented methods, computer program products and systems for analyzing at least one feature in a layout representing an integrated circuit (IC) for an overlay effect. In some cases, approaches include a computer-implemented method including: modeling a topography of the IC by running at least one of a chemical mechanical polishing (CMP) model, a deposition model or an etch model on a data file representing the IC after formation of an uppermost layer; modeling the at least one feature in the IC for an overlay effect using the topography model of the IC; and modifying the data file representing the IC after formation of the uppermost layer in response to detecting the overlay effect in the at least one feature, the overlay effect occurring in a layer underlying the uppermost layer.