El Museo Canario stores a large collection of aboriginal skulls that have been essential to the study of the origin and chronology of the population of the Canary archipelago since the 19th century. Regrettably, research has been dominated by biased and racial interpretations of both bioarchaeological and cultural evidence. When scientific racism and craniometric studies were rejected, studies of the Canarian indigenous skulls variability was also abandoned without replies. However, digital technologies and virtual sciences allow us to improve research and re-evaluate old paradigms. In this work, we present a digitalisation project aiming to construct a virtual database of the indigenous Canarian skulls, using a simple method of digitalisation that is very suitable to deal with large collections- The procedure, involving a portable 3D structured light scanner has allowed us to digitally reproduce more than 400 skulls stored at Museo Canario. This work offers a wide variety of possibilities for archaeology and anthropology. The versatility of 3D digital models enables the generation of interactive documentation, educational material for digital conservation and dissemination purposes. Indeed, 3D models are easily shared and can be displayed over diverse web-based repositories and online platforms and so, creating virtual online museums. We have created a profile in Sketchfab (https://sketchfab.com/craniacanaria2.0) where we intend to upload gradually the complete virtual collection of skulls we have realised. Moreover, digital skulls can serve as research objects. We discuss the advantages of studying 3D objects in a computerised environment, which includes traditional anthropometric studies (linear measurements and angles) but also 3D geometric morphometric approaches. In fact, in future studies, we will apply 3D geometric morphometrics for reassessing skull variation of ancient Canarians going beyond old paradigms and taking into account the latest advances in archaeology, anthropology and genetics in Canarian research. Highlights:- El Museo Canario stores an exceptional human skull collection that has served as the basis for numerous studies seeking to reveal the origin and chronology of the indigenous population.- This study presents an easy methodology for obtaining digital imagery using a 3D surface scanner, which allows constructing a virtual skull collection comprising more than 400 individuals.- Virtual 3D models have numerous advantages and applications in anthropology and archaeology, not only improving research but also permitting the re-evaluation of old paradigms.