A method and associated apparatus for topographically characterizing a workpiece. The workpiece is scanned with a scanning probe along a first directional grid, thereby scanning a reference surface and an area of interest subportion of the reference surface, at a variable pixel density including a first pixel density outside the area of interest and a second pixel density inside the area of interest to derive a first digital file characterizing topography of the workpiece. The workpiece is further scanned along the reference surface and the area of interest with the scanning probe along a second directional grid that is substantially orthogonal to the first directional grid and at a constant pixel density to derive a second digital file characterizing topography of the workpiece. A processor executes computer-readable instructions stored in memory that generate a topographical profile of the workpiece in relation to the first and second digital files.