As highly portable media, USB flash drives are easily lost or stolen. All USB flash drives can have their contents encrypted using third-party disk encryption software, which can often be run directly from the USB drive without installation (for example, FreeOTFE), although some, such as BitLocker, require the user to have administrative rights on every computer it is run on.
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Floppy disk hardware emulators exist which effectively utilize the internal connections and physical attributes of a floppy disk drive to utilize a device where a USB flash drive emulates the storage space of a floppy disk in a solid state form, and can be divided into a number of individual virtual floppy disk images using individual data channels.

With wide deployment(s) of flash drives being used in various environments (secured or otherwise), the issue of data and information security remains important. The use of biometrics and encryption is becoming the norm with the need for increased security for data; on-the-fly encryption systems are particularly useful in this regard, as they can transparently encrypt large amounts of data. In some cases a secure USB drive may use a hardware-based encryption mechanism that uses a hardware module instead of software for strongly encrypting data. IEEE 1667 is an attempt to create a generic authentication platform for USB drives. It is supported in Windows 7 and Windows Vista (Service Pack 2 with a hotfix).[47]
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Floppy disk drives are rarely fitted to modern computers and are obsolete for normal purposes, although internal and external drives can be fitted if required. Floppy disks may be the method of choice for transferring data to and from very old computers without USB or booting from floppy disks, and so they are sometimes used to change the firmware on, for example, BIOS chips. Devices with removable storage like older Yamaha music keyboards are also dependent on floppy disks, which require computers to process them. Newer devices are built with USB flash drive support.

Usually, such drives will be custom-stamped with a company's logo, as a form of advertising. The drive may be blank, or preloaded with graphics, documentation, web links, Flash animation or other multimedia, and free or demonstration software. Some preloaded drives are read-only, while others are configured with both read-only and user-writable segments. Such dual-partition drives are more expensive.[61]

Most USB flash drives do not include a write protection mechanism. This feature, which gradually became less common, consists of a switch on the housing of the drive itself, that prevents the host computer from writing or modifying data on the drive. For example, write protection makes a device suitable for repairing virus-contaminated host computers without the risk of infecting a USB flash drive itself. In contrast to SD cards, write protection on USB flash drives (when available) is connected to the drive circuitry, and is handled by the drive itself instead of the host (on SD cards handling of the write-protection notch is optional).
Motherboard firmware (including BIOS and UEFI) can be updated using USB flash drives. Usually, new firmware image is downloaded and placed onto a FAT16- or FAT32-formatted USB flash drive connected to a system which is to be updated, and path to the new firmware image is selected within the update component of system's firmware.[49] Some motherboard manufacturers are also allowing such updates to be performed without the need for entering system's firmware update component, making it possible to easily recover systems with corrupted firmware.[50]
^{Lexar is attempting to introduce a USB FlashCard, which would be a compact USB flash drive intended to replace various kinds of flash memory cards. Pretec introduced a similar card, which also plugs into any USB port, but is just one quarter the thickness of the Lexar model.[85] Until 2008, SanDisk manufactured a product called SD Plus, which was a SecureDigital card with a USB connector.[86]}
_{Quickly transfer files to and from your laptop or desktop using this SanDisk Ultra SDCZ48-064G-A46 USB 3.0 flash drive that features a read speed of up to 80MB/sec. The 64GB capacity offers ample storage space. (Ten times faster than USB 2.0 drives. Write speeds up to 10 times faster than Cruzer USB 2.0 drive.)* *USB 3.0 port required. Based on internal testing; performance may be lower depending upon host device.}
USB 2.0 flash drives have a transfer rate of up to 480Mbps, while USB 3.0 flash drives allow for transfer rates 10 times faster — up to 4.8Gbps. However, you can only take advantage of this higher speed if your device has a USB 3.0 port. Although USB 3.0 flash drives and other devices are backwards compatible with USB 2.0 ports, they will only operate at a USB 2.0 rate.