Troy besieged by messy rebels with special structures (7)
I believe the answer is:
systems
'structures' is the definition.
(system is a kind of structure)
'troy besieged by messy rebels with special' is the wordplay.
'troy' becomes 't'.
'besieged by' indicates putting letters inside (I've seen this in other clues).
'rebels with' is an anagram indicator.
'special' becomes 'S' (common abbreviation as in Special Air Service).
'messy' mixed up with 's' can make 'sysems'.
't' put into 'sysems' is 'SYSTEMS'.
(Other definitions for systems that I've seen before include "Arrangements of units that function together" , "procedures" , "Methods of working" , "Sets of interrelated parts" , "Theories of universe, perhaps" .)