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Basically, I do a lot of work from home, some of which is confidential work. My company has a policy which restricts me from using any form of 'Cloud' to back my files up, so I have set up my time machine to a partition drive on a work server. This however tries to back up my whole Macbook, but I only want to back up the folder which contains my work.

Is there anyway I can set it up to just back up the single folder, as the partition will not have enough space to back my whole Macbook up, and I also have personal files on which would not be required.

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You can specify folders to be excluded from your Time Machine backup, specifically, you could specify everything BUT your specific files. You can access this by going to system preferences > time machine > options.

For example, I have an SD card that's always in my MacBook Air missing from my time machine backup, because I prefer to keep that separated. So I added that device as excluded.

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    This is the correct way to use stock time machine. Do note that as you create new folders on the Mac, you might inadvertently back them up as well depending on where your one chosen back up folder resides. You might also look into something like Crash Plan that backs up only the folders you specify as setting up a white list is much simpler than setting up the black list as Time Machine uses. – bmike Oct 7 '14 at 14:42
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    The closer the folder you want to backup is to the root directory, the better. Then you can just exclude everything but that folder, and the exclusion extends to subdirectories. – krs013 Oct 7 '14 at 15:46
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    Also make sure that you select "show invisible items" while excluding directories, otherwise TM will back up directories you may not be aware of. – garageàtrois May 7 '15 at 15:31
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Short answer... "Get Backup 3" from the Mac Apps Store.

I'm looking for the same solution, (Or was). Basically I want to back up just one folder multiple times a day to a flash drive, similar to the way Time Machine does. BETTER YET! (Million $ idea here...) I would like a local cloud, i.e. I make a change, it updates my local backup on my flash drive to be in sync right then and there when I make the change (Like drop box does). The closest thing I have found is "Get Backup 3" on the Mac App store. You can choose an Origin folder and a destination folder and set it to synchronize the two. You can choose the direction as well which is great, : Folder A to Folder B, or Folder B to Folder A, or even Bi-Directional updates. You can also schedule sync times. I set mine up for close to the end of the day. It backs up and I leave my thumb drive at work in case my laptop ever gets stolen at least I have a copy of my files backed up (Network here is very restrictive and painfully slow).

Hope that helps.

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