This paper describes modelling of an integrated AFM - CMM instrument, its calibration, and estimation of measurement uncertainty. Positioning errors were seen to limit the instrument performance. Software for off-line stitching of single AFM scans was developed and verified, which allows compensation of such errors. A geometrical model of the instrument was produced, describing the interaction between AFM and CMM systematic errors. The model parameters were quantified through calibration, and the model used for establishing an optimised measurement procedure for surface mapping. A maximum uncertainty of 0.8% was achieved for the case of surface mapping of 1.2*1.2 mm2 consisting of 49 single AFM scanned areas.