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A few days ago, I tried installing Windows 8.1 on my late 2011 Mac by using disk utility to make a free space on my disk and a Windows 8.1 boot drive to install. While installing, my Mac recognized the boot drive as "EFI Boot" (when I pressed the options key to select the boot drive).

In the part when I had to format my partitions for installation, Windows created 2 partitions in the free space: 1. the Microsoft Reserved partition and 2. the partition where Windows is meant to be installed.

The installation went well, no errors were raised, but when I pressed the options key at startup to boot to Windows, my Mac recognized my Windows partition as "EFI Boot" (so now I have 3 options when I pressed the Options key:Macintosh HD, EFI Boot, and Recovery). That is not really a big problem to me, but then when I started using Windows, I couldn't find a way to make the audio drivers working. I couldn't install Microsoft Office either.

So, I booted into my Macintosh HD partition, and use disk utility to remove the Windows partition and the Microsoft Reserved partition. Then, I reinstalled Windows 8.1 by following these instructions: Boot camp install of Windows 7 issue, no bootable devices

Everything went well and the audio is now working, but now, when I press the Options key at startup, I have 4 options: Macintosh HD, Windows, EFI Boot, and Recovery. When I tried choosing "EFI Boot", it shows me a blue screen, saying:

Recovery
Your PC needs to be repaired
A required device isn't connected or can't be accessed.

Press Enter to try again
Press F8 for Startup settings

When I tried pressing Enter and F8 keys, it returned to the same blue screen.

When I tried mounting the EFI partition, I see 3 folders: Apple, Boot, and Microsoft. I tried deleting the Microsoft folder (and I kept the copy of it somewhere else), and boot into the EFI Boot again, my computer froze and restarted.

The question is, how can I make the EFI Boot disappear when I press the options key at startup? It's not creating any problems with my Mac or Windows partitions, but I'm very curious about what it actually is, what does it have to do with my computer, and why does it decide to show up when I pressed the options key?

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Your question has two parts. The first part is repeated below.

The question is, how can I make the EFI Boot disappear when I press the options key at startup?

This a duplicate of the question "Ghost partition, Windows BSOD". The rest of your question, which again is repeated below, does require further explanation.

It's not creating any problems with my Mac or Windows partitions, but I'm very curious about what it actually is, what does it have to do with my computer, and why does it decide to show up when I pressed the options key?

The "EFI Boot" appears because the Mac firmware finds the boot file BOOTx64.EFI in the folder \EFI\BOOT on the EFI partition of your internal drive. This is part of the UEFI specification. For example, if you go to the "uefi.org Specifications web page", you can download and view the "UEFI Specification Version 2.5". Sections 3.5.1.1 Removable Media Boot Behavior and 3.5.1.2 Non-removable Media Boot Behavior (on pages 88-90) describe the naming of the BOOTx64.EFI file and that it should appear in the \EFI\BOOT folder.

When holding down the Option ⌥ at startup, the Mac firmware will look for the \EFI\BOOT\BOOTx64.EFI file on each EFI partition of all drives accessible at startup. Each occurrence will generate an icon with the label "EFI Boot" on the Startup Manager menu.

When Windows installs, some of the startup files are stored in the folder \EFI\MICROSOFT. These files are also duplicated (with some renaming) in the \EFI\BOOT folder. Not all non-Apple operating systems do this when installing. For example, Ubuntu Linux does not. (Well, last time I installed in EFI mode it did not.) The Ubuntu installer does create a folder \EFI\UBUNTU with startup files (GRUB), which the Mac firmware by default ignores. To get Ubuntu to appear in the Startup Manager, you have to manually mount the EFI partition and copy the files in the \EFI\UBUNTU folder to the \EFI\BOOT folder. (Also, the copied grubx64.efi file needs to be renamed to BOOTX64.EFI.)

If you need to do this for two operating systems, then you will need a second EFI partition. This should not present a problem since an EFI partition is fairly small (<200 MB) and the limit on Macs by default is 128 partitions. However, to tell one operating system for the other, while viewing the choices presented by the Startup Manager, you may want to change the icons.

For example, I have rEFInd installed in a second 134 MB EFI partition on my iMac. (This happens to be the last of 9 partitions.) Additionally, I have Windows 10, Yosemite (on volume "Steelhead") and El Capitan (on volume "Steelhead2") installed. Below is a image of my Macs Startup Manager menu. (For a better view, click on the image or open in a new window.)

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The icon can be changed by mounting the EFI partition and adding the icon file .VolumeIcon.icns to the root folder. A collection of these icons, for popular Linux and other operating systems, can be found here.

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