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Whatever host architecture Linux runs on, a filesystem is required, and there will be numerous files populating that filesystem. Flash memory, if used by Linux, must be suitably formatted with a partition table and filesystem(s).
It is worth noting that if your using nand flash, nor flash, etc, you will typically be writing one or more bootloader images, a kernel image, and a rootfs image (jffs2, yaffs, units, etc). You won't write each file in the file system individually.