Methods and apparatuses are described for adaptively tracking a feature of a sample using a scanning probe microscope. The adaptive technique provides an adaptive method for tracking the feature scan-to-scan despite actual or apparent changes in feature shape due, for example, to an evolving/transitioning state of the sample, and/or actual or apparent changing position due, for example, to movement of the sample and/or drift of the piezoelectric tube actuator. In a preferred embodiment, each scan may be processed line-by-line, or subpart-by-subpart, and may be analyzed either in real time or off-line. This processing technique improves speed, processing, reaction, and display times.