I'll give you an example to answer your question.
If you create a plane, make a layer and just stamp something using a texture like this:

Then you export using Document with Alpha:

Now you'll have that layer with the alpha channel:

Also, if you need it to be as per your 2D view with all the maps applied (this takes into account your HDRi lighting) as opposed to just the diffuse texture then you can export as per the 2D view like so:
