I'd like to do a fresh install on a macbook air running 10.9.4 and manually restore programs and files from time machine.  How would I go about doing this?

In the past I've always just run a full backup from time machine, but my computer is just getting way too full and its performance is a little sluggish.   If there's any way to to just reinstall all the programs without user files, and then manually restore user files on an as needed basis, that would be ideal.
Also, should I just reinstall mavericks using the command + R function?
Any help would be appreciated.   Thanks.

Install or Reinstall Mavericks or Mountain Lion from Scratch
Be sure you backup your files to an external drive or second internal drive because the following procedure will remove everything from the hard drive.
OS X Mavericks- Erase and reinstall OS X
OS X Mountain Lion- Erase and reinstall OS X
OS X Lion- Erase and reinstall Mac OS X
Note: You will need an active Internet connection. I suggest using Ethernet if possible
            because it is three times faster than wireless.

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