Windows XP and Vista offer such conversion and there are other free sync softwares like SYNCBACK available. Be sure this is not your only backup copy. The forum is littered with questions about how to restore from such backups.
I have a portable hard drive that I would like to change from Fat 32 to NTFS. Can this be done.It is a Passport Western Digital 160GB but unfortunately has pre installed software for synchronising with OS.