1. Insert your USB pen drive. Let kernel detect it.

2. Open Terminal. And show disk partition list by run the following commands :

$ sudo fdisk -l

Then you’ll got like similar output :

Disk /dev/sda: 500.1 GB, 500107862016 bytes
255 heads, 63 sectors/track, 60801 cylinders, total 976773168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x7fe082c4

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *        2048      206847      102400    7  HPFS/NTFS/exFAT
/dev/sda2          206848   116609191    58201172    7  HPFS/NTFS/exFAT
/dev/sda3       116611072   362371071   122880000    7  HPFS/NTFS/exFAT
/dev/sda4       362373118   976773119   307200001    5  Extended
/dev/sda5       362373120   557685619    97656250   83  Linux
/dev/sda6       960391168   976773119     8190976   82  Linux swap / Solaris
/dev/sda7       557686784   960380927   201347072   83  Linux

Partition table entries are not in disk order

Disk /dev/sdb: 7803 MB, 7803174912 bytes
122 heads, 58 sectors/track, 2153 cylinders, total 15240576 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0xc3072e18

   Device Boot      Start         End      Blocks   Id  System
/dev/sdb1   *        8064    15240575     7616256    c  W95 FAT32 (LBA)

3. Take a look at your flash disk partition. Usually under /dev/sdb
On this case, my flash disk is on /dev/sdb1 (see picture above)

4. Now format the partition using mkfs.vfat command :

$ sudo mkfs.vfat -n "TOSHIBA" -I /dev/sdb1

5. Thats’s all :D

NOTE : If you got “mkfs.vfat: command not found” output, you need to install it.
For Arch linux users :

$ pacman -S dosfstools ntfsprogs

*  dosfstools gets you mkfs.vfat and mkfs.msdos
** ntfsprogs gets you mkfs.ntfs