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My scene has stuff on three layers. The layer buttons show a dot on a fourth layer, one that to my knowledge contains nothing - no meshes, no cameras, no lights or anything. If I have only that one layer active, and tap 'A' to select everything, nothing shows, just the usual grid and 3D cursor. What the heck is existing in this layer that prevents it from being empty?

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    $\begingroup$ Just to be sure, you have pressed Alt + H to make sure nothing is hidden? $\endgroup$ – JulianHzg Aug 11 '13 at 18:33
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    $\begingroup$ Can you attach the blend-file? Perhaps you have something hidden there. $\endgroup$ – iKlsR Aug 11 '13 at 18:33
  • $\begingroup$ Check your scene graph and see if anything is hidden in there. $\endgroup$ – CharlesL Aug 11 '13 at 19:02
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    $\begingroup$ When you delete a mesh in edit mode , its pivot point remains in object mode. Check your layer. Select all and press delete. $\endgroup$ – Ali Jibran Aug 11 '13 at 20:38
  • $\begingroup$ It's possible that whatever is hidden/invisible on that layer is also un-selectable. (selectability in the 3D view can be toggled in the Outliner by pressing the mouse icon) $\endgroup$ – gandalf3 Aug 11 '13 at 23:04
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Select the suspicious layer. In the Outliner, set the Display Mode to Visible Layers:

The outliner, with display modes shown

If there's anything there – hidden or not – you'll see it there.

If nothing appears, please upload your .blend file for further diagnosis.

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