How do I scan my windows partition for viruses from Ubuntu?

There is lots of bootable anti virus disks you can use, I would recommend AVG Free. AVG has over 110 million user. It provides antivirus protection for Linux/FreeBSD for free.

AVG Free is a version of the AVG antivirus which is free for private and non-commercial use. There is no graphical interface available for the current Linux versions of AVG.¹

To download click here.

Once you install, reboot the PC to initialize AVG. Alternatively you could run

sudo /etc/init.d/avgd start  

To start using AVG, just press Ctrl+Alt+T on your keyboard to open Terminal. When it opens, run the command below

sudo avgupdate

More on help.ubuntu.com

However I would suggest that you run an up to date anti-virus scanner from within your windows partition. Or you can use Bitdefender. Boot CD available here

For the top 5 Anti virus for Ubuntu. See here

^{1Source:Ubuntu Documentations}

It is possible to scan your windows partition. I recommend you do it off a live CD (32 bit).

Download and install Avast! Linux Home Edition.

Launch Avast and update its Database.

Now mount your Windows Partition.

Click on Selected folders and browse to your partition.

Click start scan.

Install ClamTk - that is a graphical frontend for ClamAV, the command line antivirus mentioned here.

Did you already try Clamav?

sudo apt-get install clamav

You said you didn't find a setting within clamAV to scan other partitions. What about:

sudo clamscan -r --move=/tmp/virus /mnt/windows-partition

to show only infected files add the -iswitch Perhaps you should do a sudo freshclam before scanning to update your virus definitions.

Though my way of solving such problems isn't related to Ubuntu, it still may be valuable.
One of the best antiviruses - Kaspersky Anti-Virus - provides a method to cure severely infected installations of Windows. They provide Rescue Disk in ISO format and it is absolutely free. It is powerful and fully functional. It is based on Gentoo distribution with KDE. You can burn it to DVD or make a bootable USB.

Boot from it (it can be run in grahical and text modes). There are several shortcuts on the desktop. Run "Kaspersky Rescue Disk", update the virus definitions, because they are old (you will need to setup Internet connection). Select the objects you wish to scan (boot sector, start-up objects, partitions) and press "Start Objects Scan" button.

This ISO can be downloaded here: https://support.kaspersky.com/viruses/rescuedisk.
On the same page you will find several guides: how to burn disk, how to use the product. These guides are detailed and pretty explanatory so I decided not to duplicate them here. Also there you can find some info regarding UEFI.

Avira also offers a rescue cd, which can be downloaded here: http://www.avira.com/en/download/product/avira-rescue-system. It is a standalone live CD. Just boot it, update the signature files, and run it. You can also install clamAV and scan your windows partitions with it if you can mount them under Ubuntu. This should be relatively safe, as it is very unlikely that you have a cross-platform virus on your windows partitions. However, it is not entirely impossible, so using a live cd is the safer option here!

Avast now supports Linux based servers only. I had a response from Avast support to similar query. The only commercial package available at http://www.avast.com/linux-server-antivirus

clamscan works for Ubuntu home as default. It can be made to scan other partitions, including windows partitions, provided you define the path properly.

I tried in the terminal:

sudo clamscan -r --move=/tmp/virus /mnt/windows-partition

The first error was about /tmp/virus. There was no such directory in my system. So I had to create it.

Then again there was an error for /mnt/windows-partition:

/mnt/windows-partition: No such file or directory
WARNING: /mnt/windows-partition: Can't access file

Workaround

The path can be found by double right clicking on the Windows partition on the left menu. Then, on the left pane, if you hover the cursor the path details are shown. Else right click on the Windows partition, left click on "Properties", then you will find in the Basic Menu "Location: /media/"volume_name" (without quotes. This will be after Name, Type, Contents) and add the "Name" of the partition on top, such as:

/media/"volume_name"/2ABC123903A129B4A

("Name_of_partition". 16 digits in my case)

I tried the following clamscan command and it worked:

sudo clamscan -r --move=/tmp/virus /media/"volume_name"/2ABC123903A129B4A

I had "Flash Pro" malware, which was choking my internet browsing both in Windows 8.1 and Ubuntu 14.04 LTS 64 bit version.

I used the approach suggested above with some minor changes

1. First make sure the partition is mounted. The easiest way to do so is to click on it in your file navigator. Also windows needs to be shut down correctly (no hibernation)

2. create a directory for FOUND items

   mkdir virusscan

3. execute clamscan

   sudo clamscan -r --copy=virusscan --bell --log=virusscan/log /media/{yourusername}/

The reason why I advise to use --copy instead of --move and then delete items, is that turn out to be malware by hand is that clamav at least in my case found a lot of false positives. If you use --move you have to copy them back by hand.

Also you can use the -i flag so that the output only shows infected files. (for more information on the command flags use man clamav)