Here is a tip to backup all your data and restore it after a fresh install (yes restore ALL the data, and pref! This is just beautiful isn't it? ).

So, if you want to make a fresh install of your system without loosing all your data and pref, the best way is to backup the entire partition where you actual mac install is located to another partition.

I used this free tool to clone mine: Clone X 3

I bought a 110€ hard drive of 1TB (yep 1TB and it's a 7200rt/min ^^). I have created some partitions and cloned my Mac on one of them

Note that you can also use Time Machine to backup your entire data!!!!! But I think this is safer to clone your entire partition

Ok then, when you did it, you can format and make a fresh install

Directly after the install (after the first boot and after some basic steps), you Mac will ask you if you want to restore your data from another Mac:

So select that you have the data From another volume on this Mac

And then it will start searching your data, when it's done you can ask to restore everything

So don't forget to backup your files!