Panda Labs is offering a FREE download (http://www.pandasecurity.com/usa/homeusers/downloads/usbvaccine/ ) that can be used on your external drives and on each pc, which will basically disable the autorun feature.  With the feature disabled, you should be able to scan your external drive, and make sure its ok, prior to it being able to cause malware havoc.

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   From the Panda Website

There is an increasing amount of malware which, like the dangerous Conficker worm, spreads via removable devices and drives such as memory sticks, MP3 players, digital cameras, etc. To do this, these malicious codes modify the AutoRun file on these devices.

Panda USB Vaccine is a free solution designed to protect against this threat. It offers a double layer of preventive protection, allowing users to disable the AutoRun feature on computers as well as on USB drives and other devices:

Vaccine for computers: This is a ‘vaccine’ for computers to prevent any AutoRun file from running, regardless of whether the device (memory stick, CD, etc.) is infected or not.

Vaccine for USB devices: This is a ‘vaccine’ for removable USB devices, preventing the AutoRun file from becoming a source of infection. The tool disables this file so it cannot be read, modified or replaced by malicious code.

This is a very useful tool as there is no simple way of disabling the AutoRun feature in Windows. This provides users with a simple way of disabling this feature, offering a high degree of protection against infections from removable drives and devices.

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Just remember that this needs to be used both on the external drives and PC.  Even if you don’t have an external drive yourself, its a good thing to run it on your pc, in case some one visits (or your kids or co-workers) and brings an external drive with them.