The structure of a material is of special significance to its properties, and has as such been an active area of research. In materials science it is desirable to learn more about how material properties at the micro level influence properties at the macroscopic level. Manual or automated analysis of three-dimensional images of material samples is a useful tool in this respect. Automated analysis has the potential to be more exact, reliable and objective than subjective analysis. In order to analyze the material structure based on digital microscopy images of the material, noise reduction and automatically identifying the parts of the image belonging to the material of interest are necessary. Measurements on fiber networks, found in paper and wood fiber – reinforced composite-materials, require a segmentation of the imaged material sample into individual fibers. Methodology and software tools for these image processing tasks are presented in this book and relevant articles in the literature are referenced. Our new method for segmentation based on tracking fibers is presented. The intended audience of this book is any interested reader with a background in science.