It is described the uncertainty analysis performed for the reconstruction of a 3D shape. Multiple stereo systems are employed to measure a 3D surface with superimposed colored markers. The described procedure comprises a detailed uncertainty analysis of all the measurement phases, and the evaluated uncertainties are employed to perform a compatibility analysis of points acquired by different stereo pairs. The compatible acquired markers are statistically merged in order to obtain a measurement of a 3D shape and an evaluation of the associated uncertainty. Both the compatibility analysis and the measurement merging is based on the evaluated uncertainty.