<p class="VARAbstract">During the 19<sup>th</sup> and 20<sup>th</sup> centuries, numerous museums, scientific societies, and royal academies were founded in Europe and America. In this scenario, the Anthropological Museum Montané was founded in Havana, Cuba. Its collection has grown over the years, thanks to researchers, antiquarians, and amateurs. Since its foundation, the Museum Montané has become an essential institution for anthropological and archaeological research in the region. Nowadays, the Museum Montané, like other museums in developing countries, faces a challenge in the introduction of state-of-the-art technologies to digitizing exhibits and the creation of innovative projects to attract visitors. The current possibilities of virtualization of cultural heritage using digital technologies have a favorable impact on the preservation, access, and management of museum collections. The use of three-dimensional (3D) models fosters engagement with visitors, stimulates new forms of learning, and revalorizes the exhibits. In the current study, we use a hand-held structured light scanner to create 3D reality-based models of pre-Columbian crania from the Caribbean and South American collection of the Anthropological Museum Montané. The resulting 3D models were used for producing 3D printing replicas and animated videos. The 3D resources derived will encourage new knowledge through research, and provide broader access to these pre-Columbian crania collection through learning and outreach activities. The significance of digitizing these specimens goes beyond the creation of 3D models. It means protecting these fragile and valuable collections for future generations. The methodology and results reported here can be used in other museums with similar collections to digitally document, study, protect, and disseminate the archaeological heritage. Going forward, we seek to continue exploring the application of novel methods and digital techniques to the study of the pre-Columbian crania collections in Latin American and the Caribbean area.</p><p class="VARAbstractHeader">Highlights:</p><ul><li><p>A hand-held structured light scanner was used to acquire 3D reality-based models of pre-Columbian crania. The 3D models resulting were used for 3D printing replicas and 3D animations.</p></li><li><p>This study provides unprecedented 3D reconstructions of pre-Columbian crania in the Caribbean area, and new 3D reconstructions of artificially deformed crania from South America.</p></li><li><p>The 3D resources created will encourage new knowledge through research, and provide broader access to these pre-Columbian crania collection through learning and outreach activities.</p></li></ul>