You can easily do it in a script, e.g. like this
# Read the trajectory. You don't need to do this if you already have the trajectory.
md_trajectory = nlread('xyz.nc', MDTrajectory)[0]
# Extract the 3rd snapshot.
bulk_configuration = md_trajectory.image(2)
(MDTrajectory has a number of other query functions that might be useful for you, see http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.mdtrajectory.html)
If you want to use the snapshot in the parts of the VNL-GUI (Builder, ScirptGenerator), you need to go through the MovieTool, though.
Does that help?[/code]