Scan data is almost never a qualified solid.
It sounds to me like you folks are not 3D modeling mavens, but more medical professionals looking to access this technology.
For that reason I strongly suggest you invest in FreeForm Modeling software from 3D systems.
Although available without a haptic arm, you really really want to spring for the haptic arm.
Ever see one of those documentaries or youtube videos of folks doing a reconstruction of a face on a computer? Or of doctors using xray scan data to print practice models of patient skulls or spines? Or prosthetic makers using a computer to model a custom orthotic?
Chance are you saw them using Freeform. Its the go to app for anyone in the medical field needing to produce solid models from scan data.
What you will like about Freeform is you do not have to be an expert in computer modeling to use it. Its learning curve is about 3 weeks. And it Can not produce a model that is not a qualified solid.
Importing scan data it will convert it to a solid- filling any holes in the data to create a solid. You can then very easily clean up the model anywhere it filled in holes to make the model correct, and even model whatever you want or alter the model in any way you can envision.
Because of its haptic interface and its voxel modeling space, you will find that anyone can quickly learn how to use the software to achieve excellent results.
Do yourself a favor, and look into Freeform. There is a reason you keep seeing it in videos of medical uses for 3D modeling.