Refactoring functionality  in the Scala IDE version 3.0.4 does not work. After a little bit of Googling I found the following website Scala Refactoring. It turns out this functionality is work in progress. However, the refactoring functionality is part of the latest milestone  of the Scale IDE. I have tried it and it works like a dream. Added bonus is the latest version of Scala IDE works with Eclipse Luna. Take it for a spin and see what you think.
 For example renaming all occurrences of a variable by selecting an occurrence and hitting Shift+Alt+R.
 Scala IDE version 4.0.0-M3.