I'm not sure what the problem is here?
Load an "Empty" template (eg keyboard Starter, which defaults to an empty workspace, with 1 Patch and a couple of Concert Level Aux's and some Inserts on the main output).
Delete the Patch, delete the 2 Aux channels and remove the Inserts on the Master output.
File:Save As Template
I hear you man! I looked up this discussion precisely with the same exact question... In fact I even watched a guy on youtube ( http://youtu.be/kWc8N2SRLDQ ) @ 2:50 do it and my mainstage does not give me the option of "new concert" like his does... It just gives me the option of "New..." and goes right to the templates... when he did it, it opened a blank template just like we both want. Does anybody else experience this?