A method of investigating a sample using Scanning Electron Microscopy (SEM), comprising the following steps: Irradiating a surface (S) of the sample using a probing electron beam in a plurality (N) of measurement sessions, each measurement session having an associated beam parameter (P) value that is chosen from a range of such values and that differs between measurement sessions; Detecting stimulated radiation emitted by the sample during each measurement session, associating a measurand (M) therewith and noting the value of this measurand for each measurement session, thus allowing compilation of a data set (D) of data pairs (Pi, Mi), where 1≦i≦N, wherein: A statistical Blind Source Separation (BSS) technique is employed to automatically process the data set (D) and spatially resolve it into a result set (R) of imaging pairs (Qk, Lk), in which an imaging quantity (Q) having value Qk is associated with a discrete depth level Lk referenced to the surface S.