How to remove an icon from launchpad that does not appear in the Finder?
If you are using Yosemite here is the surgical approach to remove only what you want to, instead of wiping out all of Launchpad.

Open up your Terminal app of choice, then use the following command:

sqlite3 $(find /private/var/folders \( -name com.apple.dock.launchpad -a -user $USER \) 2&gt; /dev/null)/db/db "DELETE FROM apps WHERE title='APP_NAME_CASE_SENSITIVE';" &amp;&amp; killall Dock


to remove an application from the Launchpad.