A method to study Cellulose Nanofibril (CNF) distribution in three dimensions within a paper matrix-in-situ-was developed. Focused Ion Beam (FIB)/Scanning Electron Microscopy (SEM) tomography was used to investigate the distribution of cellulose nanofibres in thee dimensions within a paper structure. Sufficient resolution and material contrast was contained using both secondary and back-scattered electrons in volumes as large as 103 um3. Challenges and approaches to achieve this are discussed, both with respect to the microscopy technique and with respect to image processing and volume reconstruction. A range of recorded images and reconstructed 3D volumes show the technique capable of resolving CNF in a paper matrix. Results presented show CNF within the paper matrix forming capsules enclosing filler particles. These capsules are seen to only infrequently be in physical contact with the enclosed particles. Similar separation between CNF and enclosed filler particles was tested and confirmed in CNF films with 10 wt% added ground calcium carbonate.