It's not the file that's NTFS or FAT, it's the way the drive was configured. FAT (File Allocation Table) and NTFS (New Technology File System) are file systems. A certain way that the drive reads the files. So all you have to know is what File System your source and destination drives are. If you go to "My Computer" and select a drive, on the bottom you will see "File System" and it will tell you what it is.
Like mentioned, it doesn't matter. You can copy files from one system to another - either way.