I suspect what you really want to do is apply a "code cleanup" to ALL of your java source files, not just ones that you selected manually.
Here's how:
1) In the Packages view (or the Package Explorer view) change your "Package Presentation" from "hierarchical" to "flat". There's a little upside down triangle in the top right corner of each view that lets you change this setting.
2) Now when you navigate to your source code directory you should see ALL the packages and sub packages and sub sub packages that contain your java source files, all presented together in one (possibly huge) list.
3) Of course, when you have a huge list like this, you can easily select all the packages (left-click the first one, then shift left-click the last one).
4) Then, right click on the selection, and go to "Source->Clean Up..." (or any other "Source" submenu item, like "Organize Imports") and the dialog that pops up will tell you how many source files it is about to change.
Hope that helps!