A system for estimating front side overlay on a sample based on shape data is disclosed. The system includes a characterization sub-system and a controller. The controller includes one or more processors configured to: generate a vacuum hole map of a vacuum chuck; generate a vacuum force distribution across a sample based on the generated vacuum hole map of the vacuum chuck; determine shape data of the sample based on the vacuum force distribution and an identified relationship between backside surface roughness and vacuum force of the vacuum chuck; and convert the shape data of the sample to an overlay value of a frontside surface of the sample.