This paper describes a combination of an automated image acquisition method and a probabilistic tracking method for analysis of the 3D microstructure of a sheet of paper. A prototype which combines microtomy and light microscopy enables efficient and fully automated digitization of paper samples in high resolution. A particle filter based tracking method then allows to segment individual fibers from the obtained 3D data sets. The capability of accessing the properties of individual fibers enables analysis of e. g. 3D fiber mass distribution, 3D fiber orientation or fiber morphology. Experiments show that the method provides results consistent with the knowledge of paper experts.