I too have the same question as jwise. My reason for asking comes from the fact that I am a new user and as such created a project that is junk. I have successfully created a good project since and would like to remove the junk from my project list.
You can delete the .AIP(project file) which are not needed from their location on the disk. However, can you please give me more details about your specific scenario? Maybe attach a printscreen so I can have a better view about this?