Guys Ctrl+Alt+Shift+E is used if you wish to simply merge all visible layers. However... if, as mention somewhat by Gaussian, you wish to create a composite layer, you can more simply merge layers that have been linked.
One note about that though...
Any layers that you wish to NOT include in the composite, simply do not link it with the others. And the fact that a document has a Background layer should have no effect on this. If it does/did for you, then you most likely mispressed the keys to merge the layers (
you pressed Ctrl+Shift+E), or did not have the new empty layer active when merging.
Here once again, and with one extra fact, are the steps to merge a group of layers down to a single new layer:
1) Create a new empty layer and move it anywhere you wish within the layer stacking order.
2) Now, Link all the layers that you wish to be merged together, to the new empty layer. Most importantly, the new empty layer must be the active layer. And all layers you don't want merged, should not have a chain link next to them -- and this would include the document's Background layer also.
3) With the new empty layer active, simply press Alt+Ctrl+E (Mac: Option+Cmd+E). This will copy all linked layers and merge them onto the new empty layer.
HINT #1: Keep in mind also that it is not fundamental to use a new empty layer. This can also be done using any layer you want. Just bear in mind that once merged, the active layer will not be copied -- it becomes the final composite layer.
HINT #2: All layers being merged
must also be visible, as well as being linked together.
HINT #3: Using the above "linking layers" method is the exact same as using the "merge all visible layers" method -- which was all we had before layer linking came along. The differences are this:
- A) Layers to be merged/composited are made visible & invisible; instead of being Linked (including the document's default BG layer).
B) The quick-key combo is different -- PC: Ctrl+Alt+Shift+E /// Mac: Cmd+Option+Shift+E.
Other than that though, it produces the exact same results.[/list:u]So there it is, again... i just wanted to shine a little more clarity on this tip, because it's a very useful one. Thanks Gauss.
PS: And please don't forget that this, and any other info concerning merging layers can be easily found within the Help Files.