An apparatus can include a logic element configured to generate information corresponding to an adaptive layer to be formed over a current substrate based at least in part on a difference in flatness profiles associated with a first substrate chuck and a second substrate chuck. In another aspect, a method can include obtaining a difference in thickness profiles for the first and second chucks using a prior substrate, and forming an adaptive layer over a previously formed patterned layer of a current substrate and before forming a patterned resist layer aligned to the previously formed patterned layer. In an embodiment, the thickness profile of the adaptive layer is a function of the inverse of the difference in flatness profiles of the substrate chucks. The adaptive layer can help to reduce overlay error associated with different flatness profiles of substrate chucks.