Windows-8_1Installing Windows 8.1 from a USB Stick under a UEFI BIOS and Secure Boot.
When Building a Windows UEFI system there are a few things to know that are different from when building an old BIOS based machine. First your USB install stick has be be formatted with FAT32 and Not NTFS. Second your UEFI motherboard probably has a Compatibility Support Module (CSM) mode that is set for BIOS compatibility. You need to turn that off if you want to enable UEFI, Secure Boot, and booting from a GPT partitioned disk.

The 11 steps for manually preparing / building a USB Disk to be a bootable Win 8.1 Install.
This bootable USB stick will work for both older BIOS installs as well as the newer UEFI installs.

1. Diskpart (Run from a CMD prompt)
2. List Disk
3. Select Disk # (Where # is the number of your USB disk)
4. Clean (removes any partitions on the USB disk, including any hidden sectors)
5. Create Partition Primary (Creates a new primary partition with default parameters)
6. Select Partition 1 (Focus on the newly created partition)
7. Active (Sets the selected partition to an active valid system partition state)
8. Format FS=fat32 quick (Formats the partition with the FAT32 file system. FAT32 is needed instead of NTFS so that it can load under the secure boot UEFI BIOS.)
9. Assign (Assigns the USB drive a drive letter)
10. Exit
11. Copy all the files from the Windows 8.1 DVD to the USB Stick.

 

For More information on on UEFI and Installing Windows to these machines here are some links:
Happy System Building! –Brian

For more information on UEFI BIOS and Secure Boot in Windows 8.1
http://answers.microsoft.com/en-us/windows/forum/windows8_1-security/uefi-secure-boot-in-windows-81/65d74e19-9572-4a91-85aa-57fa783f0759

Installing Windows on UEFI-based Computers
http://technet.microsoft.com/en-us/library/hh290675(v=WS.10).aspx#BootingUEFImode