Select a visible layer at the top of your layer stack. press ctrl/cmd-alt/opt-shift-E. This will make a flattened layer of all your visible layers without actually flattening your file. Then make a selection of the layers that you want to merge by pressing ctrl/cmd and clicking on the layer icon. If you are doing more than one layer, hold the shift key down also for the next selection. After making a selection, select the stamped merged layer, described in the first step and press ctrl/cmd-shift-J. This will put your selection on a new layer. You can then delete the stamped merged layer described in the first step. It will make a layer with transparency.
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