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I'm giving my external HDD to a friend tomorrow for a few days. It's partitioned via Master Boot Record and there are two partitions: a NTFS partition and my Time Machine partition. I don't want him to be able to access the latter, but I can't turn the encryption on because the disk would have to be partitioned with GUID.

Changing the partition scheme would require me to reformat the disk. I can't do this either, as I don't have another HDD to put my files on in the meantime.

Is there another way to encrypt the partition, other than the built-in option of OS X? Or is there a way to prohibit access to the Time Machine partition without any encryption at all?

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I think what you could do is creating a encrypted disk image on the external HDD and put your time maschine files in it for the timeframe your friend has the disk. To achieve this open the disk utility tool and choose File -> New -> Blank Disc Image (or Image From Folder).

BUT keep in mind that as long as this disk is not (re-)formatted properly it will be easy to recover unencrypted data which seems to be deleted or moved (using some fancy recovery tools).

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Perfect, thank you. I had to remove a bunch of old backups to free some space. Wow, this is really a chore with Time Machine. No problem that the data could be recovered. I'm not assuming he would pry around in my stuff, it's a friend after all. I just don't like the feeling of anyone having full access to all my data. –  Tom Feb 6 '13 at 15:03
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