How to do a Clean Install of OS X.

There are many reasons why you would want to do a clean install of OS X. Here are a few of   them:

• After replacing your Hard Drive with a larger capacity one;
• After replacing your Hard Drive because it failed;
• After replacing your Hard Drive with an SSD;
• After adding a second hard drive in an Optibay;
• After a major software issue;
• Just because you want to clean up your Mac properly.

By doing a clean install you will end up with a fresh installation of OS X. One of the main reasons why you would want to do a clean install, instead of restoring your old system, is that you’ll get rid of all the unused junk that accumulated over the years. You could call this a nice spring cleaning.
Before we continue, please note that a clean install will erase all of the contents on your drive so you’ll need to back up all your important files, settings and Apps before proceeding. A time machine backup is usually more than enough.
 
Creating a Bootable Flash Drive
In order to install OS X, you’ll need to boot from another drive where all the installation files will be located; a minimum of 8Gb is required. You can use any USB stick or external Hard Drive to do so. Please note that you’ll need to erase all of the external device’s content so you might want to stick with an 8Gb thumb drive.
1.  Go on the Mac App Store to download the latest version of OS X (at the time of writing, it is 10.13 - High Sierra).
2. Download the App called DiskMaker X to assist you in the creation of the USB Thumb Drive. Follow the assistant prompts. It will ask you which version of OS X you want to install, where the file is located and which external drive you want to use.
 
Restart and Install
Now we move on to the Installation process:
1. Restart your Mac with the Thumb Drive connected and hold down the Option (Alt) Key. You should get to a screen that allows you to select the Thumb Drive and boot from it.
2. Select the Disk Utility App to initialise/erase the drive you’re going to put the OS on. Just select the new drive in the left column, then use the erase tab to format the drive. If you have multiple drives/partitions, please make sure you select the right one as an error here might be fatal for your data.
3. Close the Disk Utility App to get back to the OS X Utilities list and select Install OS X.
 
Import all your Data
Now that you have a clean OS we would recommend not to use the Migration Assistant to import all of your data as this will bring back all the unwanted junk as well.
1. It is worth taking the time to install all of your Third Party Applications from scratch as this will also guarantee that you have the latest updates available.

a. Start with the Mac App Store, just log in with your account and go into the Purchases tab to reinstall any Apps that you have previously purchased.

b. Then you’ll probably need to go and download all of the other Apps that you want from their respective websites. Another suggestion would be to try to stick with as few Apps as possible. You might realise that at the end of the day you only need a few extra Apps and not the ten dozen you used to have.

c. If you still have some installers on CD or DVD that can’t be found online, we’d recommend that you create an image of them so that you can keep a copy on your backup drive as well. You can use the Disk Utility App for this.

2. For your personal files (documents, photos, videos, music, etc.), we would suggest to manually copy and paste them into the desired folder. This is to keep everything as clean as possible.
Quick Tip : Some Apps, like iTunes, might need to be directed to the right folder after the transfer. To do that, just hold down the Option (Alt) key when starting iTunes and you will be prompted to choose a library file.