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FAT32 is a drive organization scheme, it doesn't matter whether your processor is 16, 32, 64, or 128 bits. You need to use FAT32 if you're going to make a DOS-bootable flash drive, but you'll be limited to a flash drive no larger than 32 GB; you cannot format a larger partition than 32 GB with FAT32. If you need that much space then you must use NTFS, and you won't be able to use plain old DOS to access it.
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