Precise probe placement in automated scanning probe microscopy systems

A scanning probe microscope (SPM) system and associated method. The SPM system having a probe adapted to interact with nanoscale features of a sample and scan within a target region to produce a three-dimensional image of that target region, the system maintaining location information for a plurality of features of interest of the sample according to a sample-specific coordinate system, wherein the SPM system is configured to adjust positioning of the probe relative to the sample according to a SPM coordinate system, the SPM system further configured to manage a dynamic relationship between the sample-specific coordinate system and the SPM coordinate system by determining a set of alignment errors between the sample-specific coordinate system and the SPM coordinate system and apply corrections to the SPM coordinate system to offset the determined alignment errors.