FTM 2012. Though forget the procedure I believe it could be done in FTM Version 16.
Go to Main Toolbar(File, edit, etc).
Select Edit, Manage Facts (near the bottom)
You will get a pop up window with a list of facts on the left, and a list of commands on the right (Close, Help, etc)
Find the custom fact that you wish to delete.
When you highlight that fact the delete button will appear at the bottom of the list. click and say you are sure.