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There are many options.
1. Copy the necessary files with Explorer or take (write) a copy script.
2. Compress with an archiver or attach a script to it.
3. Put some program for backup. A bunch of such software can be found in Google by keywords.
4. Make an image of a flash drive. There are many programs, for example, Win32 Disk Imager or Ultraiso
If the flash drive is bootable, then you need to use something like dd.
1. USB Image Tool
2. Win32DiskImager
3. WinDD
4. Norton Ghost
The output from these utilities is a complete bit-for-bit image.
What does flash drive backup mean? Is it just data on it? It turns out it's just files and folders.
Take any free archiver, here's a backup for you.
7zip is here to help.
On Win, I liked this open-source program of a mega-cool kid - DSYNCHRONIZE
DSynchronize is a stand-alone utility that let you periodically synchronize two or more folders on Hard Disk, Floppy Disk, LAN, USB Key, CD-DVD (with packet writing software) and FTP server.
It is also possible to specify the time and the day to schedule the synchronization to run, and to create some additional "filters" for other factors.
Real-Time sync is also supported.
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