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In the projects pane in the Source Packages the packes are normally like this org.me.myapp Class1 Class2 org.me.myapp.excaptions Exception1 Exception2 When you change it to tree view (right click background->view java packages as) you get org me myapp exceptions Exception1 Exception2 Class1 Class2 I would prefer this (best of both worlds) org.me.myapp exceptions Exception1 Exception2 Class1 Class2 Also when having multiple packages starting with the same folder (com.sun and com.google) Those two should be separated (where by default using the above rule there would be google and sun both under com)