I have an stl-file with a 3D scan of a small unmanned aerial vehicle that I want to use in a physics simulation software, but before I can use it I need to clean it up a bit and fix non-manifolds. The model has over 600.000 faces, so it is not easy to manipulate by hand. Furthermore the 3D scan of the vehicle includes some of the interior of the vehicle that I am not interested in, since it would complicate the aerodynamics unnecessarily. So I was hoping for a way to create a new model based on the surface of the complex model.
I have included a image of the front of the vehicle from Blender with holes to the interior colored red. 
I should probably also mention that I am completely new to Blender.