During counter-scanning two surface scans, viz. the direct scan and the counter scan, are obtained. The counter scan starts at the point where the direct scan ends. This point is called the coincidence point (CP). With the counter scan, the probe movement along the raster line and the probe movement from one raster line to the other are carried out along the opposite directions to the movements in the direct scan. The obtained pair of images are called counter-scanned images (CSIs).

When the raster distortions are linear, i.e., when the drift velocity is constant, to correct drift, it is sufficient to measure the coordinates of only one common feature in the direct and the counter scans. In case of nonlinear distortion, when the drift velocity varies during the scan, the number of common features on CSIs whose coordinates need to be measured increases in proportion to the degree of the nonlinearity.

Typically, the drift of the microscope probe relative to the measured surface consists of two components: one is associated with creep of the scanner piezoceramic, the other is caused by a thermal deformation of the instrument due to change in temperature. The first component is nonlinear (it can be approximated by logarithm), the second component can be considered as linear in most practical applications.

The use of the counter-scanning method makes it possible, even in the case of a strong drift leading to errors in tens of percents, to measure the surface topography with error of few tenths of a percent.