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X-ray Computed Tomography (CT), a commonly used technique in a wide variety of research fields, nowadays represents a unique and powerful procedure to discover, reveal and preserve a fundamental part of our patrimony: ancient handwritten documents. For modern and well-preserved ones, traditional document scanning systems are suitable for their correct digitization, and, consequently, for their preservation; however, the digitization of ancient, fragile and damaged manuscripts is still a formidable challenge for conservators. The X-ray tomographic approach has already proven its effectiveness in data acquisition, but the algorithmic steps from tomographic images to real page-by-page extraction and reading are still a difficult undertaking. In this work, we propose a new procedure for the segmentation of single pages from the 3D tomographic data of closed historical manuscripts, based on geometric features and flood fill methods. The achieved results prove the capability of the methodology in segmenting the different pages recorded starting from the whole CT acquired volume.