A sample analysis system includes a scanning electron microscope, an optical and/or eBeam inspection system, and an optical metrology system. The system further includes at least one controller. The controller is configured to receive a first plurality of selected regions of interest of the sample; generate a first critical dimension uniformity map based on a first inspection performed by the scanning electron microscope at the first selected regions of interest; determine a second plurality of selected regions of interest based on the first critical dimension uniformity map; generate a second critical dimension uniformity map based on a second inspection performed by the optical and/or eBeam inspection system at the second selected regions of interest; and determine one or more process tool control parameters based on inspection results and on overlay measurements performed on the sample by the optical metrology system.