Cloning the ISO 9660 systemīut if you clone from an Ubuntu iso file to the USB pendrive, you need not worry about the boot sector/method, everything will be cloned, and you get a 'hybrid' system with an ISO 9660 system which includes the boot sector 'automatically'. If you are talking about an installed Ubuntu system (like into an internal drive, but in this case in a USB drive), then you can select both MBR alias MSDOS partition table and GPT alias GUID partition table, but it will be easier with MBR. Rufus is an extracting tool with a good reputation. If you are talking about a live Ubuntu system, yes, MBR alias MSDOS partition table is recommended, for example if you use Rufus in Windows.
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