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Delete All Hidden Layers in Adobe Photoshop

When you have hidden layers in Photoshop which you want to delete permanently use command from Layers menu without to search and select them first. There is no need to have any layer selected, just visit Layer > Delete > Hidden Layers and confirm on Yes button in new dialog which will appear.
Delete all hidden layers in Adobe Photoshop
Delete all hidden layers in Adobe Photoshop

Filter only hidden layers in Layers palette in Photoshop CS6 
In new CS6 version of Adobe Photoshop you can display or filter only hidden layers in Layers palette. First choose for filter type: Attribute then from second field choose Not Visible. Only hidden layers will be listed on Layers palette, select them and delete using Delete key on your keyboard or by right clicking and choosing Delete Layers. You can also use and Layer > Delete > Hidden Layers. Advantage of filtering not visible layers is that you can check which layers are hidden before to delete them all. In order to see layer content on layers thumbnail check Large Thumbnail and Layer Bounds in Layers Panel Options dialog.
Filter layers by attribute Not Visible
Filter layers by attribute Not Visible

Reference:
Photoshop Help / Managing layers
Photoshop / Layer basics

Product used in this tutorial: Adobe Photoshop CS5 Extended, Adobe Photoshop CS6

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