We propose a new method to support tympanoplasty operations for ear, nose and throat (ENT) surgery, namely the reconstruction of the eardrum. This intervention needs precise distance and contour measurements to allow a successful operation. Currently, surgeons only have limited tools to measure patient specific anatomy and rely on their experience and visual judgement to estimate anatomical dimensions. Therefore, we provide an image-based augmented reality (AR) measuring tool using a complete digital processing chain, giving instant feedback about anatomical structures with high metric accuracy. Our method detects the center of gravity of a marked spherical instrument tip in the stereoscopic image pair of a digital surgical microscope and triangulates points in 3D space of the calibrated stereo system. We track the tip using a self-updating template-matching algorithm. An accurate subpixel refinement of the tip center prevents drift and guarantees highly accurate stereo correspondences. GPU implementation and a color-based pre-detection allows real-time tracking in high-resolution images. Reconstructed trajectories form a true-scale virtual stencil, which is projected directly into the surgeon’s field of view as a precise registered AR overlay. This overlay supports the surgeon while cutting a patient specific shape from autologous tissue. Measurement accuracy and real-time tracking performance are evaluated using a depth-of-field test body and a temporal bone model, where the obtained 3D path-reconstruction is compared to a CT scan. Our approach provides great potential to improve state-of-the-art surgical workflows by reducing operating times and facilitating intraoperative decisions.