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Can we assume you want to do this in the process of copying the whole thing to someplace else and maintain alignment?
I don't think there's really a direct way to do it, but I know I've built a trick into an action at some time in the past when I needed to do a copy/paste and maintain alignment... As I recall, I selected all, saved the selection, expande the canvas 1 pixel in each dimension, then used the inverse of the saved selection to fill the additional pixel border with a color that was not transparent. Then a select all and copy got everything and I was able to trim off the excess later because I knew it was one extra pixel on each of two sides.
Another approach might be to convert the transparency to a mask. Photoshop CS5 offers a direct way to do this. Layer - Layer Mask - From Transparency.
A bit more info about what you're trying to achieve might help but if you have Photoshop CS5 then try using Edit->Paste Special->Paste in Place instead of the normal Paste.
Sorry for the late answer , I`ve been busy yesterday.
So - I have like 50 png files which have a graphic element in the center and the rest is transparency, when I select the whole rectangle (the png) and when I try to paste/paste special it gives me the element in a square selection , without preserving the entire empty space (transparency).
Are you pasting into an existing document or making a new document from the selected area?
Maybe Duplicate Layer would work. (right click on the layer thumbnail in the layers panel to get Duplicate Layer.
You'll have to use workarounds for this like making a new layer, filling it with some color and then copying both of them to your final document using Layer->Duplicate Layers. You can also use Layer->Link Layers to make sure that those layers will always move together and then delete the extra layer when you're done compositing your final image.