Method of monitoring at least one of an overlay or an alignment between layers of a semiconductor substrate, scanning probe microscopy system and computer program

A method of monitoring at least one of an overlay or an alignment between a first and a underlying second layer of a semiconductor substrate using a scanning probe microscopy system, wherein the method comprises:

• scanning the substrate surface, using a probe tip of the scanning probe microscopy system, in at least one scanning direction, for obtaining a measurement of a first topography of the first layer and of a second topography of the underlying second layer in the at least one scanning direction said probe tip receiving an acoustic signal provided from a transducer and having propagated through the substrate;
• generating at least one pattern template and matching the measured first topography with the at least one pattern template for determining a first candidate pattern to represent the measured first topography in the at least one scanning direction;
• correlating the first candidate pattern with the measured second topography for obtaining a second candidate pattern to represent the measured second topography in the at least one scanning direction;
• determining, from the first candidate pattern, one or more feature characteristics of device features in the first topography;
• determining, from the second candidate pattern, one or more feature characteristics of device features in the second topography;
• and
• calculating, using the determined feature characteristics of the first and second topography, one or more overlay parameters or alignment parameters.