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Windoes 11 23H2 build 22631.3155 Ventoy 1.097 when creating ventoy usb with ether proteced mode on or off, MBR or GPT does not create
any subdirectories on samsung 64 gig usb drive
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Ventoy only formats Partition 1. No files or folders are created. This is normal.
If you want your ISO files to be in a folder, then simply create the folders that you want yourself.
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When using Windows, Windows may not show the 2nd VTOYEFI partition (it hides it and does not give it a drive letter).
So you may see the USB drive in Windows Explorer as just D: or E: or another letter.
So just copy your ISO files to that drive.
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There is no reason to access the vtoyefi partition, it should not be changed.