As Hyper-V Server 2008 R2 is based on core and has no GUI, I used command prompt and Windows Server Backup (wbadmin).
1) Check Windows Server Backup is Installed. In command prompt, type oclist
2) Run the following command to perfrom a system backup of all critical volumes with system state
wbadmin start backup -backuptarget:E: -allcritical -systemstate
(E being the portable storage device I have plugged into my host where I want the backup to be stored on)
3) Backup is complete!