The root directory of any drive is where all other directories branch from. The root directory of a computer's hard drive is the C: directory. There is no such specific designation for flash drives.
A, B and C Drives
Drive letters (and therefore root directories) are designated by the computer. A and B drives are always saved for floppy drives, and the C drive is saved for the primary hard disk of a computer. After that, drive letters are not consistent from computer to computer.
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Additional Drive Letters
Any hard disk aside from the primary drive, is assigned to D, and so on. Optical disc drives are next, followed by USB devices. So on a computer with one hard drive and a DVD burner, the root of the USB flash drive will be E. If the computer has two hard drives, or an additional disc drive, then the USB flash drive will be assigned F.
Whatever the root drive of your USB flash drive is, it rarely matters. It will function the same way regardless of its drive designation. The only time it might matter is if something is installed to the USB drive and then that drive letter changes with the addition of new hardware. If the operating system expects a program to be in one drive, and it is not, that can cause errors and the program will likely not run correctly.