If you install many programs on your Mac, then in a similar way to managing Apps in iOS devices, you can click and drag the various icons in LaunchPad on top of each other to create folders containing them. With such folders created, you ought to be able to undo them by simply removing items from them and when the second to last item is removed, the folder should disappear; however, a bug exists in OS X where this may not happen, leaving you with a number of empty folders that will not disappear from your system, and may progressively clutter LaunchPad.

LaunchPad may show only empty folders once items have been taken out, leaving you with a cluttered organization.
This problem likely is occurring because of a problem with the LaunchPad database, which is a separate index managed by the Dock that catalogues your various applications. As with many such databases in OS X, the ones for LaunchPad are small Sqlite3 databases that can be opened in many Sqlite3 reader programs; however, the root of this problem may be a small nuance corruption in the database that will likely be difficult to track down. As a result, your best bet for fixing the issue is to simply reset the database and start over from scratch.
1. Create screenshots
2. Reset the database
Go to the Applications > Utilities folder in the Finder and open the Terminal, followed by running the following command:
defaults write com.apple.dock ResetLaunchPad -bool true; killall Dock
This command is actually two, the first of which writes to the Dock’s preferences file and flags the LaunchPad to be reset the next time the Dock is launched. The second will kill the current instance of the Dock, which will spur OS X to relaunch it immediately. These together will reset your database, and should clear the problem at hand.
3. Remove the database files
If the command above does not fix the issue, then again in the Terminal run the following command, which will clear out the database files themselves and force OS X to recreate them from scratch. Again, this is two commands, with the first one that clears the files and the second one that re-launches the Dock:
rm ~/Library/Application\ Support/Dock/*.db; killall Dock
Note that this last command will also remove the database for your Desktop picture, so after running it you will have to go to the Desktop & Screen Saver system preferences to set your desktop picture again.
Thanks a lot, it works!
It works, but then the problem comes back again when I install new programmes
yes, just keep it in evernote and use it every time.
pure awesomeness.. thanks
there should be a 1 click option of this in a dmg file that someone should make and download install freeware defaults write com.apple.dock ResetLaunchPad -bool true; killall Dock i pasted it in the terminal and it worked better than end task of explorer.exe in windows.
defaults write com.apple.dock ResetLaunchPad -bool true; killall Dock is so good and it works. i will keep it in evernote and use it every time and next time.
open automator. create application. search library, shell. paste the terminal command. save. close. run it. command + down.