Is nothing on the counter but a line on the map (6)
I believe the answer is:
isobar
'a line on the map' is the definition.
(I've seen this before)
'is nothing on the counter' is the wordplay.
'nothing on' becomes 'o' (I've seen this in other clues).
'the counter' becomes 'bar' (bar is a kind of counter).
'is'+'o'+'bar'='ISOBAR'
'but' is the link.
(Other definitions for isobar that I've seen before include "One showing pressure" , "What's shown on some maps" , "Line of equal barometric pressure on a map" , "It connects points of equal air pressure" , "meteorologist's line" .)