Right click on the project root and select Source -> Format. This should work for at least version 3.8.1. and above.
If the above does not work, you're probably using an older Eclipse-version. In such case you can select your Source Folders by clicking on them while holding down CTRL, then select Source -> Format from the right-click -menu. Works with package-folders and class files also, in case you don't want to format the entire project.