Computer tomography (CT) is a common tool in palaeontology, allowing researchers to revisit old descriptions of problematic taxa in unprecedented detail. However, the nature of fossilisation can decrease the effectiveness of traditional radiological approaches. Here we provide new cranial reconstructions of various thalattosaurs using state-of-art tomographic approaches to accommodate for the specific preservational characteristics of their fossil remains. Thalattosauriformes are secondarily aquatic reptiles from the Triassic. This enigmatic clade is characterized by high morphological disparity, particularly in their body sizes, rostral shapes and dentition types. This has raised numerous questions about their functional ecology and potential competition with more abundant marine reptile clades. In addition, their phylogenetic position remains unclear. We focused on the highly flattened specimens from Monte San Giorgio (Middle Triassic, Switzerland/Italy) and some new and more 3D finds from the Middle and Late Triassic of China and North America. We employed a combination of traditional CT and Computer Laminography (CL) to solve the problem of low-resolution output when scanning large flattened specimens. We then created complete 3D cranial models using segmentation, re-positioning, and retrodeformation. This new approach not only offers detailed morphological information for phylogenetic purposes, but also provides 3D data to be used in quantitative shape analyses and detailed biomechanical studies. In this manner, the functional ecology of thalattosaurs and their position relative to the other marine reptile fauna within the foodweb of the Monte San Giorgio region can be studied.