The Japan Nuclear Cycle Development Institute (JNC) is undertaking research into the deep geological environment in Japan in the Tono area of Japan. In the Mizunami Underground Research Laboratory (MIU) Project, located in the Tono area, JNC is carrying out surface-based investigations and will excavate an Underground Research Laboratory (URL) in order to establish comprehensive techniques for investigating and characterising the geological environment. The MIU Project focuses on the investigation of the granitic rocks of the Toki Granite. The geological structure and hydrogeological properties of the Toki Granite are closely affected by the regional fracture zones and faults. The interpretation of these features is undertaken in 3D and directly linked into 3D hydrogeological models. Significant uncertainty exists in the 3D interpretation of the fracture zones, and geologists must make several assumptions regarding the 3D structure in order to develop the 3D interpretation. In order that these assumptions are communicated to the hydrogeologists, a methodology has been developed for representing uncertainty in the 3D geological models. An important part of the uncertainty representation, is the development of a fracture zone classification in which the uncertainty in both the presence and the geometry of the fracture zone is assigned. Other elements include the development of alternative models, visualisation of raw data, development of conceptual models, development of bounding models, and suitable quality assurance and archiving of modelling projects.