 Solution

Flattening removes fitted components of the image whether they are instrumental or real. A true specimen slope, broad dome or slow height variation can be erased if it resembles the chosen background. Strong features can bias a fit and create false depressions, streaks or halos; an overly flexible polynomial can fit away scientifically useful topography.

Line-by-line correction can destroy real differences between terraces, especially when no common flat region spans the lines. Height statistics, roughness and feature depths then depend on masking and fit order. Report those choices and compare profiles before and after processing.

Flattening does not restore structures inaccessible to the tip, undo a double-tip artefact, remove finite-tip broadening, reconstruct a saturated signal or recover data lost to unstable feedback. It also does not calibrate the scanner. These limitations are important when a superficially smoother image is mistaken for a more accurate measurement.