A method, system and program for determining a position of a feature referenced to a substrate. The method includes measuring a position of the feature, receiving an intended placement of the feature and determining an estimate of a placement error based on knowledge of a relative position of a first reference feature referenced to a first layer on a substrate with respect to a second reference feature referenced to a second layer on a substrate. The updated position may be used to position the layer of the substrate having the feature, or another layer of the substrate, or another layer of another substrate.