Clonezilla, the open-source program that creates and restores images of your hard disks -- recognizes nearly every file system, and works for both internal and external hard drives. If Clonezilla does not recognize your external USB drive, the problem is most likely with the drive itself. However, some configuration issues may cause Clonezilla not to see your external hard drive.

Attachment Order

You must attach the USB drive you want to use with Clonezilla before you reboot the computer and start up the software. If you try to attach the USB drive after Clonezilla has already started, it will not recognize the device. If you have created a live USB with Clonezilla instead of a bootable CD, you may need to configure your BIOS so that your computer boots from the correct USB drive.

USB Problems

The simplest solution is usually the correct one -- and when it comes to USB devices, computers most commonly do not see them due to small issues. Switch the drive to a different USB port. Check that the drive is securely plugged in; if your drive comes with a light, see if it is turned on. For external drives with removable cables, make sure you use the correct cable when connecting your USB drive, as not all USB cables provide enough power to access an external drive. If possible, connect the drive to a different device to see if it works.

Virtual Machine Settings

Virtual machines present some extra quirks when using Clonezilla with external hard drives. If you are trying to create disk images for a virtual machine, or are moving data to one, before booting up Clonezilla, connect the USB drive you want to manage, and then enable it for your virtual machine. Make sure that the drive is not mounted on your host machine -- the physical operating system -- before you enable it to avoid improper unmounting and data loss when it connects to the virtual machine. Like with a physical machine, the hard drive must be connected before you boot up Clonezilla.

Drive Source

If Clonezilla runs from a live USB drive instead of a CD, you will not be able to modify that USB drive unless the space is partitioned. Disk utilities cannot change active partitions, which is why you have to boot from external media to format, repartition or clone your main hard drive. If you to run Clonezilla from the same drive you need to partition, use a disk management utility such as GParted or Parted Magic (see Resources) to create two partitions on the disk, and then commit Clonezilla to one of the partitions. When you boot up Clonezilla, it will recognize the second partition on the drive as its own disk.