Is there a way to get the exterior surface of a complex model in Blender? 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.
There are at least three ways to do this. One is to select the whole object, and apply the decimate modifier; another is to create a pair of planes, one above and one below, and apply to the planes a shrinkwrap modifier. The third method is to use the retopology idea offered by @poor. However, while any of these might yield suitable results, they each require a certain level of mastery of Blender to be able to do. In my view, you'd be well served to spend some time mastering Blender, before you attempt what you are trying to do.