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HOW-TO: Format USB Flash Drives to NTFS
By default, Windows doesn't allow USB flash drives (in this document we will shorten its name to UFD) to be formated to NTFS. I'm quite puzzled by this myself but as this is the default behavior, you will need to discover and study a bit more in order to get the functionality you require. Further research brought the realization that this limitation only exists on the GUI. If you are used to the *nix systems command line coding, this will suit your taste quite well.
Diskpart is an integral part of Windows, a command line utility to partition disks -- quite similar to fdisk of the Linux world. While this is not a full-blown command-line coding like *nix, it is a bit similar in a sense. Enough talk.. on to the meaty details of diskpart.
Plug the UFD on an available USB port and launch "cmd.exe" as Administrator. You will know that the command tool ran as Administrator due to the "Administrator" tag on the upper left corner of the window (see below).
The procedure below should be done on the cmd.exe window as posted above. The "DISKPART>" prompt is provided for illustration purposes to show that the commands used need to be executed inside th diskpart shell (in performing the procedure, skip the "DISKPART>" portion when copying and pasting).
 Launch diskpart. On the command tool key-in "diskpart" (or "diskpart.exe").
 On the diskpart prompt, key in "DISKPART> list disk". The last one should be the UFD. You may also check the size column just to be sure. Then select that disk by "DISKPART> select disk 1". If you have many disks select the appropriate number "disk X", where X is the disk number.
[3*] (optional) You may choose to clean the disk partitioning information using "DISKPART> clean". This will delete everything in the drive so be careful! A prompt of successful cleaning will follow.
[4*] If you skipped STEP#3 above, you already have a partition on the UFD. Create a partition on the disk. Use command "DISKPART> create partition primary". Verify that a primary partition exists using "DISKPART> list partition".
 Then select the newly created partition using "select primary 1".
 Mark the partition active through command "DISKPART> active". When you list the partitions, the "*" (asterisk) before the partition number indicates that the partition is active.
 Format the UFD, "DISKPART> format fs=ntfs" or "DISKPART> format fs=ntfs quick".
[8*] (optional) If you wish to assign a drive letter to the UFD, use "DISKPART> assign".
 Exit the diskpart utility. "DISKPART> exit".
Yes, the command line utility is really cool. It can give you the flexibility you need if the GUI doesn't give room for it.
Typing the commands above can be excruciating and tiring if you're not used to it. Don't worry about this though as you can shorten the commands. You may key-in the first three letters of the command.
For example, instead of "DISKPART> list partition" you may use "DISKPART> lis par". The commands execute the same set of instructions and is less of a hassle to type.
To get a better explanation of what a particular command does, you can always use help (DISKPART> help select).
This procedure is easy to execute on a computer system with only a system drive and UFD. On a system with multiple disks and UFDs this can be really risky.