A partition can be formatted to different file systems. For a pen drive FAT partition is adopted universally. Linux partition is commonly ext3/ext2/ext4/reiserfs.
Windows is work with FAT or NTFS filesystem.
For formatting a partition as FAT ( as in the case of a pen drive ), give the command
mkfs.vfat /dev/sdb1
where /dev/sdb1 corresponds to the required partition. To get partition number plug in the device, mount it (automatic), get the number from /etc/mtab.
Note: The partition should have unmounted before formatting it.
Similar commands for formatting other systems are mkfs.bfs,mkfs.ext2,mkfs.minix,mkfs.reiserfs,mkfs.cramfs,mkfs.ext3,mkfs.msdos,mkfs.vfat
GUI tools for formatting a partition are gparted (for Gnome) and qtparted (for kde).
