What carries motorway, note, through separate part of mountain (6,6)
I believe the answer is:
severn bridge
'what carries motorway' is the definition.
(the Severn Bridge carries the M48 motorway)
'note through separate part of mountain' is the wordplay.
'note' becomes 'nb' ().
'through' is an insertion indicator (inserted letters go through the word).
'separate' becomes 'sever' (sever can mean to split or separate).
'part of mountain' becomes 'ridge' (geographical feature).
'sever'+'ridge'='severridge'
'nb' placed within 'severridge' is 'SEVERN BRIDGE'.
(Other definitions for severn bridge that I've seen before include "Route from England to south Wales" , "M-four river crossing" .)