Metrology systems, tools, and methods that characterize one or more layers of a microelectronic workpiece are disclosed herein. In one embodiment, a system for characterizing thickness and topography of a workpiece layer includes a layer thickness instrument configured to measure a thickness of a first workpiece layer at individual sampling sites, a surface topography instrument configured to measure a relative surface height of the first layer at the individual sampling sites, and a processing unit communicatively coupled to receive thickness and topography measurements and operable to output layer data that includes individual thickness measurements combined with individual topography measurements at workpiece coordinates corresponding to the individual sampling sites. In another embodiment, the system further includes an output device communicatively coupled with the processing unit and operable to graphically display a stratigraphic cross-section corresponding to the output layer data.