3D multi-band/multi-spectral reconstruction is a technique, which allows the use of images taken in different spectral bands for the reconstruction of spectrally-resolved 3D models of paintings. In this work, we propose a procedure for constructing and comparing 3D multi-band models obtained starting from a variety of input data (RGB and IR images, UV-induced fluorescence images, etc.) and/or acquired with different instruments. The procedure has been tested on two case studies, with the aim to highlight the critical issues associated to the specificities of the subject and of the environmental constrains: a 14th century panel painting signed by Barnaba from Modena, preserved at the Museum of San Matteo in Pisa, Italy and a 15th century panel painting preserved at the Regional Gallery of Palazzo Bellomo in Syracuse, Italy. RGB, IR and UV–VIS fluorescence models obtained with a conventional digital camera (RGB and UV) and a multisband camera (IR) were realized and compared, for revealing differences at sub-millimeter level.