How do I make a clipping mask whilst preserving sub layer structure?

Hi guys,
I am editing a map and need my map split into multiple rectangular segments. My map is made up of many layers and sub layers which I need to preserve. When I clipping mask the map with a rectangle all of the map's subs layers merge into one layer. How do I make a clipping mask whilst preserving sub layer structure? It seems like a 'layer mask' is the correct tool but doesn't seem like CS6 has it?
Cheers
Mat

I avoid sublayers, because they really were never thoroughly developed, and when you open files, you get all your layers flipped open.
So for me paste in front works great for pasting a mask directly above the element you want to mask. Unfortunatley paste in front does not work well with sublayers so you will need to drag the mask down into the the sublayer. But atleast if you have a complex document with many sublayers, the paste in fornt gets you close.
eg; Mask is in clipboard, I select sublayer Illinois
After doing a paste in front, the mask (star shape) is not in the sublayer, but above
Drag the star shape down one in to the sublayer Illinois, select entire sublayer(use radio button right of the layer name)
and make clip mask

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