A modular X-ray scanning system was developed, to fill in the gap between portable instruments (with a limited analytical area) and mobile instruments (with large analytical areas, and sometimes bulky and difficult to transport). The scanner has been compared to a commercial tabletop instrument, by analysing a Portuguese tile (azulejo) from the 17th century. Complementary techniques were used to achieve a throughout characterisation of the sample in a complete non-destructive approach. The complexity of the acquired X-ray fluorescence (XRF) spectra, due to inherent sample stratigraphy, has been resolved using Monte Carlo simulations, and Raman spectroscopy, as the most suitable technique to complement the analysis of azulejos colours, yielding satisfactory results. The colouring agents were identified as cobalt blue and a Zn-modified Naples-yellow. The stratigraphy of the area under study was partially modelled with Monte Carlo simulations. The scanners performance has been compared by evaluating the images outputs and the global spectrum.