Order check on empty surgery (6)
I believe the answer is:
system
'order' is the definition.
(I've seen this in another clue)
'check on empty surgery' is the wordplay.
'check' becomes 'stem' (both can mean to control or stop).
'on' is a charade indicator (letters next to each other).
'empty' means to remove the middle letters.
'surgery' with its middle removed is 'sy'.
'stem' put after 'sy' is 'SYSTEM'.
(Other definitions for system that I've seen before include "Set of parts creating working whole" , "Functioning set of interactive parts" , "Method, set of connected things" , "Complex whole; method" , "Ordered scheme" .)