My Acer Aspire One D250 Laptop has dual boot Windows XP and Ubuntu 10.10 configured and installed. On the Ubuntu I usually insert most of the USB flash drives and external hard drives from the USB ports to view files since Ubuntu is known for being virus free.
However sometimes I decide to scan the USB thumb drives/ external hard drives in Ubuntu, BUT there is no per-installed anti virus software in Ubuntu. After few googling I found AVG anti Virus.
AVG has this free desktop antivirus which is cool.
I downloaded mine here http://free.avg.com/download.prd-alf and installed it. To scan from the terminal I typed sudo avgscan, if you need to update the antivirus you type in the terminal sudo avgupdate.
To scan you flash drives type sudo avgscan /media/ and the drive name if you know or just leave it as it is.
If you want to install AVG with a GUI go to here http://free.grisoft.com/doc/5390/.
More instructions on the AVG with GUI is found here http://www.howtoforge.com/avg_antivirus_ubuntu_feisty