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The detection of latent fingerprints can be a great aid in determining the authenticity of ancient artworks. In fact, a commonly used technique for the authentication of artworks consists in the comparison of fingerprints present on the surface of an artifact with other available latent fingerprints of an artist. This kind of analysis is particularly important for the authentication of clay artifacts. The clay, in fact, is often modeled barehanded, causing a great number of fingerprints left on the surface. In many cases, the artworks are very valuable or fragile and the latent fingerprints cannot be acquired using classical forensic methods. For this reason, contactless acquisition techniques have been proposed. Most of these techniques are based on the use of a single camera. In single-view acquisition systems, however, it can be difficult to properly estimate the size of the captured area, the obtained images can suffer from problems related to perspective distortions, and a calibration task cannot be performed in all the cases. In this paper, we propose a two-view acquisition system able to capture the latent fingerprints left on a clay artwork, and to compute their three-dimensional metric reconstruction. The obtained results show that the proposed approach is feasible and the reconstructed models provide a metric, view-independent, and less-distorted reconstruction of the fingerprint. In particular, we describe the application of the proposed method on a specific clay artwork associated by experts to the famous sculptor Antonio Canova (Italy, 1757-1822).