To UEFI-boot from a Windows 7 64-bit ISO (Win 7 32-bit UEFi is not supported by Microsoft), or Windows 8/8.1/10 32-bit and 64-bit ISOs, you must first convert each ISO to a FAT32 .imgPTN file using MakePartImage and the MPI_FAT32 Desktop shortcut. Do not use the MPI_NTFS Desktop shortcut because that will not UEFI-boot!
Your E2B USB drive can be formatted as FAT32 or NTFS (although exFAT and ext2 would also work as long as the .imgPTN files can be made contiguous!).
If the .imgPTN files are larger than 4GB, the E2B USB drive should not be formatted as FAT32.
Typically, the E2B USB drive is prepared as an NTFS USB drive, but the .imgPTN files are created using MPI_FAT32.
If any file inside the ISO is larger than 4GB, then see here for solutions.
Windows 7 32-bit and earlier Windows OS's do not support UEFI-booting.
Note: E2B v1.75+ allows you to add .imgPTN files to the \_ISO\WINDOWS\xxxx folders (except for the XP folder).
The Windows 7 64-bit UEFI boot problem!
Unlike the later Windows Install ISOs, the Windows 7 64-bit standard Microsoft ISO does not contain the correct UEFI boot file that is required for USB disk booting (it only supports DVD booting).
To UEFI 64-bit boot, the file \EFI\BOOT\BOOTX64.EFI must be present.
Use Split_WinISO.exe to add the boot file
You can use the Split_WinISO Windows utility (by Chandra) to automatically add the missing bootx64.efi file and make a .imgPTN file...
Download Split_WinISO.exe and copy the .exe file to the MPI folder (Split_WinISO is already included in later versions of MPI).
Run Split_WinISO.exe and click the ISO button to select your Windows 7 x64 ISO
Click on the MPIbutton to convert the ISO to a FAT32 .imgPTN file - if you do not see the MPI button then you did not copy the .exe file to the MPI Tool Kit folder!
Manually change the boot files
First, check if the file '\EFI\BOOT\BOOTX64.EFI' is in your ISO (or inside .imgPTN file). If it is not present then it will not UEFI-boot from a USB drive and we need to obtain the file and add it to our .imgPTN file.
Run E2B and select the Windows 7 64-bit.imgPTN file that you have already created using MakePartImage. You can do this by running \_ISO\SWITCH_E2B.exe or run the 'QEMU_MENU_TEST (run as admin).cmd' script on the E2B USB drive until you see the Windows 64-bit CSM menu in the QEMU window and then quit QEMU and Eject the USB drive using the Windows System Tray icon, then re-connect it.
The contents of the E2B USB drive should now comprise of the Windows 7 64-bit payload.
If the '\EFI\BOOT\BOOTX64.EFI' file is missing, you can obtain and copy the file to the USB drive by using one of the two methods below:
If you have access to a Windows x64 system, copy the file C:\Windows\Boot\EFI\bootmgfw.efi to the USB drive's \EFI\BOOT\ folder and rename the file to \EFI\BOOT\BOOTX64.EFI.
The file bootmgfw.efi can also be extracted from a Windows 7 (or higher) x64 Install DVD. It is located in the 2.7 GByte+ large archive \sources\Install.wim (and in the \sources\boot.wim file too usually) which should now be on your USB drive. The file can be extracted using an archiving program such as 7Zip. This file is usually located in the subdirectory "1" of the archive at 1\Windows\Boot\EFI\ under 7Zip. Copy the file to the USB drive's \EFI\BOOT folder and rename the file to \EFI\BOOT\BOOTX64.EFI
The USB drive should now be UEFI-bootable and you should see the CSM menu now inform you that the BOOTX64.EFI file is present and also see a Clover boot option.
Note: The Virtual Box 'BIOS' does not support UEFI-booting of Windows 764-bit - the animation will just stop (Win8 and later work OK). However, you can try booting using the Clover menu entry in E2B CSM mode which usually works under VBox.
Still will not boot?
It should not be necessary, but if it fails to UEFI-boot, also copy the whole \EFI\MICROSOFT\BOOT folder to the \EFI folder (see screenshot below).
The partition contents of the USB drive should now look like this (note the \EFI\BOOT\BOOTx64.efi file must be present).
Adding Intel USB 3.0 drivers to Windows 7
Windows 7 install ISOs do not support USB 3.0 ports or controller chips, so if you want to boot from a USB 3.0 port, you will usually need to add the USB 3.0 drivers (tip: sometimes just using a USB 2.0 port will work but sometimes it will not!).
Once you have made the .imgPTN file, you can 'switch' to it and then run the Intel Windows 7 USB 3.0 Creator utility. This will modify the install.wim and boot.wim files and add the Intel USB 3.0 drivers. Note that this utility only adds the Intel USB 3.0 drivers for Intel chipsets; it does not add non-Intel USB 3.0 drivers (e.g. AMD).
There is also a video showing how to modify an ISO or USB drive here.
Tip: I find it easier to boot from any recent Windows Install ISO that supports USB 3.0 (e.g. Win 8.1 or Windows 10), and then run WinNTSetup.exe and install the Windows 7 ISO using WinNTSetup. There is no need to modify the Windows 7 64-bit ISO if you use this method. You can then install the USB 3 and other drivers once Windows has been installed.