The dataset compiles the .raw file and details of the CT scan. The specimen was scanned at the University of Zurich and shows the holotype of Concavicaris submarinus, a thylacocephalan. PIMUZ37349 presents preserved eyes, putative muscles, gills and structures interpreted as ovaries. The mimics file includes the segmentation of the specimen, with each structure and their 3D reconstruction. The .stl files of each segmented element are available to visualise them in 3D.