A method is described intended for distributed calibration of a probe microscope scanner consisting in a search for a net of local calibration coefficients (LCCs) in the process of automatic measurement of a standard surface, whereby each point of the movement space of the scanner can be defined by a unique set of scale factors. Feature-oriented scanning (FOS) methodology is used to implement the distributed calibration, which permits to exclude in situ the negative influence of thermal drift, creep and hysteresis on the obtained results. The sensitivity of LCCs to errors in determination of position coordinates of surface features forming the local calibration structure (LCS) is eliminated by performing multiple repeated measurements followed by building regression surfaces. There are no principle restrictions on the number of repeated LCS measurements. Possessing the calibration database enables correcting in one procedure all the spatial distortions caused by nonlinearity, non-orthogonality and spurious crosstalk couplings of the microscope scanner piezomanipulators. To provide high precision of spatial measurements in nanometer range, the calibration is carried out using natural standards - constants of crystal lattice. The method allows for automatic characterization of crystal surfaces at room temperature. The method may be used with any kind of scanning probe microscope (SPM).