I've been scouring the Blender Python API docs for a way to get access to the mesh data that is displayed in the view-port. (with modifiers applied - WYSIWYG)
For reference, this was possible with the 2.4x API's
The option to apply modifiers is common for exporters included with Blender, so you can check how they do it.
Typically you can use the
It's important to remove the mesh, unless you have explicitly assigned it to an object. Otherwise it will be stored in Blender until the file is saved and loaded again.