Although an increased usage and development of 3D technologies is observed in healthcare over the last decades, full integration of these technologies remains challenging. The goal of this project is to qualitatively explore challenges, pearls, and pitfalls of AR/VR/3D printing applications usage in the medical field of a university medical center. Two rounds of face-to-face interviews were conducted using a semi-structured protocol. First an explorative round was held, interviewing medical specialists (8), PhD students (7), 3D technology specialists (5), and university teachers (3). In the second round, twenty employees in high executive functions of relevant departments were interviewed on seven statements that resulted from the first interviewing round. Data analysis was performed using direct content analyses. The first interviewing round resulted in challenges and opportunities in 3D technology usage that were grouped in 5 themes: aims of using AR/VR/3D printing (1), data acquisition (2), data management plans (3), software packages and segmentation tools (4), and output data and reaching end-user (5). The second interviewing round resulted in an overview of ideas and insights on centralization of knowledge, improving implementation of 3D technology in daily healthcare, reimbursement of 3D technologies, recommendations for further studies, and requirement of using certified software. An overview of challenges and opportunities of 3D technologies in healthcare was provided. Well-designed studies on clinical effectiveness, implementation and cost-effectiveness are warranted for further implementation into the clinical setting.