If you want to make a clean install, then you can't keep your files. Before installing Mountain Lion, make a backup of your files on an external drive with Carbon Copy Cloner or Time Machine.
Then, you will have to make a bootable Mountain Lion external drive. To do it, first download OS X Mountain Lion from the Mac App Store. Then, when the download finishes, use Lion Diskmaker > http://liondiskmaker.com
To start from the USB drive or DVD with Mountain Lion, hold the Option (Alt) key while your MacBook is starting, and select this DVD or USB drive.
After starting, open Disk Utility, choose "Macintosh HD" in the sidebar, go to Erase tab and erase the drive. Close Disk Utility and reinstall OS X.
Finally, you can restore the backup or you can restore your files manually if you didn't make a backup. You will have to reinstall the applications manually in this case. Note that if you restore the backup, you will have the same system as before installing Mountain Lion, so it's better to do an upgrade