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Background. A difficulty in computer‐assisted interventions is acquiring the patient's anatomy intraoperatively. Standard modalities have several limitations: low image quality (ultrasound), radiation exposure (computed tomography) or high costs (magnetic resonance imaging). An alternative approach uses a tracked pointer; however, the pointer causes tissue deformation and requires sterilizing. Recent proposals, utilizing a tracked conoscopic holography device, have shown promising results without the previously mentioned drawbacks. Methods. We have developed an open‐source software system that enables real‐time surface scanning using a conoscopic holography device and a wide variety of tracking systems, integrated into pre‐existing and well‐supported software solutions. Results. The mean target registration error of point measurements was 1.46 mm. For a quick guidance scan, surface reconstruction improved the surface registration error compared with point‐set registration. Conclusions. We have presented a system enabling real‐time surface scanning using a tracked conoscopic holography device. Results show that it can be useful for acquiring the patient's anatomy during surgery.