We identified tomographic reconstruction of a scanning electron microscopy tilt series recording the secondary electron signal as a well-suited method to generate high-contrast three-dimensional data of intermediate filament (IF) networks in pancreatic cancer cells. Although the tilt series does not strictly conform to the projection requirement of tomographic reconstruction, this approach is possible due to specific properties of the detergent-extracted samples. We introduce an algorithm to extract the graph structure of the IF networks from the tomograms based on image analysis tools. This allows a high-resolution analysis of network morphology, which is known to control the mechanical response of the cells to large-scale deformations. Statistical analysis of the extracted network graphs is used to investigate principles of structural network organization which can be linked to the regulation of cell elasticity.