In this work, two historical flutes of the late eighteenth century were analysed by means of X-ray computed tomography (CT). The first one is a piccolo flute whose manufacturer is unknown, though some features could suggest an English or American origin. The second musical instrument is a baroque transverse flute, probably produced by Lorenzo Cerino, an Italian instrument maker active in Turin (Italy) in the late eighteenth century. Analyses carried out provided information on manufacturing techniques, materials and conservation state, and are suitable to plan restoration intervention. In particular, through the CT images, it was possible to observe the presence of defects, cracks, fractures and previous restorations, as well as indications of the tools used in the making of the instruments. Particular attention was directed towards extracting metrological information about the objects. In fact, this work is the first step of a study with a final aim of determining an operative protocol to enable the making of precise-sounding copies of ancient instruments starting from CT images, that can be used to plan a virtual restoration, consisting in the creation of digitally restored copies with a 3D printer.