A practical method is described to find automatically the calibration coefficients and residual nonorthogonality of a tunneling microscope scanner. As initial data, the coordinates of three atoms were used forming a triangle in a highly oriented pyrolytic graphite surface appearing in the form of a spatially geometrical measure. A recognition procedure is described which can be applied to determine the lateral coordinates of the atoms. Length and orientation distortions were calculated, estimates of calibration errors were given and the requirement on the nonorthogonality limit was formulated for manipulator a given that ensures measurements of the predetermined accuracy. The sensitivity of the method to a noise in atom coordinates was determined. Experimental data showing the practical suitability of the method developed are presented. ©1998 American Institute of Physics.