Flash drives typically come formatted with the FAT32 file system, which nearly all operating systems can read, so they're generally ready to run out of the box. Operating systems also have formatting tools to clear flash drives.
Users can manually format their flash drives. Windows and Apple's OS X allow users to access the "Format" menu from their respective file explorers; this brings up a program that guides users through the process. In general, this process creates a FAT32 image. However, accessing the drive through the Device Manager on Windows computers allows users to select the more advanced NTFS filesystem, although doing so can lead to compatibility issues with Apple and Linux operating systems.
Most operating systems view flash drives as standard disk drives, which allows advanced users to use partitioning tools for less common tasks. While CDs and DVDs are still used for installing operating systems, the ubiquity and reusability of flash drives make them popular for this purpose as well.
Windows offers the DiskPart command line tool; Linux and OS X users can use the dd tool instead. These programs can write disk images directly to the drive and allow users to install any file system supported by the operating system. As a result, people who use OS X or Linux devices exclusively can take advantage of advanced features these file systems provide.