This just hurts my brain, and inflames my OCD! So, while there are a couple of nice options to clean-up LaunchPad (i.e., Launchpad-Control (free), and Launchpad Cleaner ($4.99)), I much rather man-handle it with outmost prejudice, and most impractical way possible — here is how:

Open your favorite Terminal application cd ~/Library/Application Support/Dock [...]