Security emptied trunk in procedure (6)
I believe the answer is:
system
'procedure' is the definition.
(a procedure is a system or practice)
'security emptied trunk' is the wordplay.
'emptied' suggests removing the centre.
'trunk' becomes 'stem' (I can't explain this - if you can you should believe this answer much more).
'security' with its centre taken out is 'sy'.
'sy'+'stem'='SYSTEM'
'in' acts as a link.
Can you help me to learn more?
(Other definitions for system that I've seen before include "The government" , "Arrangement of things working together" , "set-up" , "Set of things in a connected whole" , "Network" .)