In the 3D window, all Stories are projected by default, but you can limit the projection using the “Stories to Show in 3D” controls at View > Elements in 3D View > Filter and Cut Elements in 3D. Choose the range of stories you wish to display in 3D.
The Trim Elements to Story range checkbox (in the same dialog box) means that the model will be clipped at the story range boundaries. If this box is not checked, the model will not be clipped, and all elements that fall at least partially inside the story range will be displayed.
The story display in the 3D window, as set in the Filter Elements dialog box, will naturally affect the 3D Documents created from this 3D source.
For more information, see Filter and Cut Elements in 3D.