Backup procedure for a Virtual Appliance (VMWARE) Installation
Suspending the virtual machine and backing up the files with whatever backup software should do the trick. After backing up resume the virtual machine to work on it again.
Note: You will have to shut down the AS Virtual Machine completely, and possibly exit out of the vmware program.
Vmware uses .vxd (extension may vary) files to store the OS, and if vmware is running them, or running at all, then these files are in use and cant be copied.
See Also: This URL talks about using snapshots which are not recommended for extended backups but can be used to save the state of a session temporarily.