Bitdefender Antivirus for Unices works nicely with recent versions of Ubuntu. It even works well on a persistent LiveUSB when ridding a Windows system of an infection. Older Ubuntu should work in theory but you may need some updated libs.
Here's how to getting it up and running.
Download Bitdefender Antivirus for Unices trial version.
Open up a terminal and do the following:
~$ cd Downloads
~$ sudo sh ./BitDefender-Antivirus-Scanner-7.6-4.linux-gcc4x.i586.deb.run
Follow the on-screen instructions. Open up Bitdefender Scanner from Applications->System Tools menu, update and you're ready to go.
Bitdefender for Unices allows you to request free personal use activation keys right from the UI. Click on the link that says "Get a new FREE license key for personal use" right below the "Set new key" button and you'll be taken to the key request page. Simply provide a valid email address and a new key will be sent to your email.
Click on "set new key" and type or paste the given key to get a year's worth of BitDefender for personal use.
F-Prot on Ubuntu LiveUSB
How to remove malware from Windows
Technician's toolbox - malicious software removal tools