May I suggest using Carbon Copy Cloner to backup your hard drive, it is quite nice.
To remove the system directories like var/ etc/ ...
1. Right click the hard drive, and choose Get Info
2. Open the Owership & Permissions tab
3. Select Ighore ownership on this volume.
You should now be able to delete the dirs.
The reason you normally can't delete them is because they are owned by root. If you do a HD backup by dragging files in the finder, permissions shouldn't be a problem. I assume you used software to do the backup, and this software preserved permissions.
Carbon Copy Cloner does an excellent job making an exact mirror of your disk, if you are serious about backing up everything it is a great tool. Most of us only bother to backup our work directories, reinstalling Mac OS X in the event of a disaster is not that hard.
Have fun
