There is provided a system and method of examining a specimen. The method comprises obtaining an actual measurement in response to scanning the specimen using a set of scanning parameters with predefined values; obtaining a simulated measurement based on design data; comparing the actual measurement with the simulated measurement to identify a deviation with respect to a predefined tolerance; identifying at least one structural property as root cause of the deviation by: obtaining one or more additional actual measurements in response to scanning the specimen using one or more varying values of at least one scanning parameter; and providing the actual measurement and the additional actual measurements to a simulation model representative of simulated measurement distribution in a multi-dimensional property space characterized by the structural properties of the plurality of layers and the at least one scanning parameter, thereby identifying the at least one structural property.

Techniques for inspecting a substrate can include scanning the substrate across a plurality of scan positions using an interrogation beam having a width substantially equal to or greater than a diameter of at least one surface feature on a surface of the substrate to generate scanning results. A set of raw centroid calculation results can be generated based on the scanning results. An error property can be determined and removed from the raw centroid calculation results to generated refined centroid calculation results. A characteristic of the surface feature can be determined based on the centroid calculation results.