The 'in situ' investigation of different biological, chemical, physical, and environmental processes often requires the knowledge of these sample characteristics with high-(sub)micro-meter-resolution as a valuable complement to the average bulk information. Different microprobe techniques can meet these requirements and their possible combinations would offer the opportunity of thorough study of a given sample or a scientific problem. Although some of the existing software packages allow for multivariate statistical treatment of data-sets obtained by a given experimental technique, none of them permits a simultaneous statistical treatment of datasets obtained by different experimental techniques, e.g. by simultaneous scanning μ-XRF (X-ray fluorescence) and μ-XRD (X-ray diffraction), or measured at several set-ups/beamlines/synchrotrons /laboratories (e.g. combined μ-IR and μ-XRF spectroscopy). The goal of this paper is to describe in detail a sequence of operations which can be applied to multi-technique datasets for obtaining a complete set of sample characteristics and to show that at present this can be realised automatically.