Linux file systems aren't known to get infected by viruses. If you have a pendrive that has a NTFS file-system, the virus would have come from a computer with a Windows operating system. Either way the only way to truly rid yourself of malicious software is to format the drive. You didn't really give us enough information to help you there. You can start by telling us how you know you have a virus on a pendrive.

Pendrive's don't carry registry or system files that are usually what makes a virus a difficult task to get rid if. You can plug the pen drive into a linux machine and run some scans on it using Clam AV http://www.clamav.net/lang/en/