Its better to remove your windows viruses before wiping your harddisk...
As you may know ,Guttman says that you need to wipe your harddisk 25 times write to zero to ensure that your harddisk is clean...
Anyway, It is possible to scan your windows partition..
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.
After you remove the viruses... Now you can install Ubuntu cleanly
Note that: Even you keep viruses it will never affect your ubuntu(linux) but i just mention the antivirus just to clean your hdd.