A system has been developed to assess the feasibility of using motion tracking to enable pre-surgical margin mapping of basal cell carcinoma (BCC) in the clinic using optical coherence tomography (OCT). This system consists of a commercial OCT imaging system (the VivoSight 1500, MDL Ltd., Orpington, UK), which has been adapted to incorporate a webcam and a single-sensor electromagnetic positional tracking module (the Flock of Birds, Ascension Technology Corp, Vermont, USA). A supporting software interface has also been developed which allows positional data to be captured and projected onto a 2D dermoscopic image in real-time. Initial results using a stationary test phantom are encouraging, with maximum errors in the projected map in the order of 1-2mm. Initial clinical results were poor due to motion artefact, despite attempts to stabilise the patient. However, the authors present several suggested modifications that are expected to reduce the effects of motion artefact and improve the overall accuracy and clinical usability of the system.