First of all, what do you mean by pane? Eclipse has:
- Windows (Eclipse itself, e.g. instance)
- Documents (tabs)
- Views (properties, tasks, explorer, etc)
If by 'pane' you mean document editors, you have problems either with your Eclipse version or most likely one of the installed plugins.
Each View also can be closed (except maybe some project types (perspectives) of which I'm not aware). For CDT (C/C++) you can close practically everything.
I'll recommend you download latest Eclipse version with no plugins, extract it to different folder, and check if that happens again. If yes, please explain more in details (like Eclipse version, perspective you are using, any side plugins, etc).
Also a good places are Eclipse community forum, mailing list and bugz