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I just got my WD 3 TB hard drive. I put it in an external dual disk duplicator (max USB3) and partitioned and formatted it GUID with partitions of 2.2 TB and 800 GB. The larger partition was for Time Machine backup for my iMac.

I then transferred the new drive to an older external case (USB2, FW400, FW800 & eSATA). That device would only see the 800 GB partition in Disk Utility, and it would see it as a disk, not as a partition. I tried moving the 3 TB drive to another external case (USB3) and it would show me the 800 GB and the 2.2 TB partitions as disks.

I put the hd back in the original duplicator and used Disk Utility to create one partition of 3 TB. Testing the previous two other external housings they showed the exact results as in the previous paragraph. They were NOT seeing the newly made 3 TB partition, but seeing the two partitions as disks.

I opened my desktop computer, connected the hd. Windows 7 saw the 3 TB drive as a large 3TB partition and a small 200 MB EFI partition. The EFI partition was not removable. I tried using the command line Diskpart to remove all the partitions and change the partition table to MBR. The EFI partition would not budge.

On a MacPro computer the hd was seen as a normally formatted single partition 3 TB drive. On a second try it saw the two partitions as disks. OS X's diskutil showed the partitions as disks as well. For good measure I reformatted the drive again to a single partition 3 TB drive. I took note that Disk Utility did not allow me to change from GUID to MBR.

The net result was after many attempts to remedy the curious EFI partitioning table issue, showing different partitioning schemes dependent on the device that they were in. This is very scary re trusting my data to it. How can I fix or remove the EFI partition and start all over again?

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Do you have access to some Linux box? – mvp Oct 9 '13 at 4:52

If you have access to some Linux box, attach your drive as secondary drive to it. If you do not have access to Linux box, download PartedMagic and boot from CD or from USB stick with PartedMagic.

Once you started GParted (using some Linux box or PartedMagic CD or USB), choose your 3TB drive from list of drives and create new GPT partition table. Default partition table format is MBR, but for 3TB drive you need GPT in order to make use of all usable capacity.

Then, inside GPT create either one big 3TB partition, or set of smaller partitions - just the way you like it.

Now, you should be able to make use of this drive in Windows as one 3 TB partition, without having any EFI junk present on it.

Regarding using this 3TB drive in USB enclosure. Unfortunately, many USB enclosures perform their own mass storage simulation level and have trouble with relaying sizes over 2TB.

However, you should be able to use eSATA enclosures without any trouble for any drive size.

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You're seeing the effects of two issues:

First, external enclosures often alter how disks are perceived by the computer. In particular, many external enclosures translate groups of eight 512-byte sectors into 4096-byte sectors. They do this so as to enable MBR to be used on larger disks. (Given 512-byte sector sizes, MBR maxes out at 2TiB, or about 2.2TB.) I've also recently heard of enclosures that make a single over-2TiB disk look like two smaller hard disks, each of which must be partitioned separately. It sounds like your enclosures are doing different types of translation -- none at all, 512-to-4096-byte sector conversion, and maybe splitting-the-disk conversion. The solution to this problem is to prepare and use the disk in the enclosure in which it will be used, and to never change the disk's enclosure. If this is impossible for some reason, you'll need to carefully research your enclosure to be sure it matches whatever hardware you use to prepare the disk.

Second, OS X's Disk Utility automatically creates an EFI System Partition (ESP) on every disk that it prepares using the GUID Partition Table (GPT). Disk Utility hides this partition from the user's view, though. Some other partitioning tools do the same thing. Thus, the ESP can appear and disappear from view depending on what tool you use to partition the disk. Personally, I prefer to use tools that show me an accurate view of the disk. The best tool I'm aware of on this score is my own GPT fdisk (gdisk, cgdisk, and sgdisk), which is cross-platform (Linux, OS X, and Windows); however, these tools are command-line and manipulate only partitions, not the filesystems within partitions. GParted is a GUI tool that can manipulate filesystems, and it doesn't hide the ESP, but it's Linux-only and it imperfectly maps GPT data structures into a more generalized partitioning model. There are third-party GUI Windows and OS X tools, too, but I'm only passingly familiar with them, so I can't make any specific recommendations about them.

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