Apart from chemoradiotherapy, surgery by total mesorectal resection is currently the only curative therapy for colorectal cancer. However, this often has a poor outcome, especially if there are affected lymph nodes too close to the resection boundary. The circumferential resection margin (CRM) is defined as the shortest distance from an affected region to the mesorectal fascia (MF), and should be at least 1 mm. However, this 3D distance is normally estimated in 2D (from image slices) and takes no account of uncertainty of the position of the MF. We describe a system able to estimate the location of the MF with a measure at each point along it of the uncertainty in location, and which then estimates the CRM in three dimensions. The MF localisation algorithm combines anatomical knowledge with a level set method based on: a non-parametric representation of the distribution of intensities, and the use of the monogenic signal to detect portions of the boundary.