A method and apparatus for process control in the processing of a substrate is disclosed in the present invention. Embodiments of the present invention utilize a first analysis tool to determine changes in a substrate's geometry. The substrate geometry data is used to generate sampling plan that will be used to check areas of the substrate that are likely to have errors after processing. The sampling plan is fed forwards to a second analysis tool that samples the substrate after it has been processed. It is emphasized that this abstract is provided to comply with the rules requiring an abstract that will allow a searcher or other reader to quickly ascertain the subject matter of the technical disclosure. It is submitted with the understanding that it will not be used to interpret or limit the scope or meaning of the claims.