Girl accepts military organisation has structure (7)
I believe the answer is:
anatomy
'structure' is the definition.
(I have seen 'Bodily structure ' mean 'anatomy' so perhaps 'structure' could also mean 'anatomy')
'girl accepts military organisation' is the wordplay.
'girl' becomes 'amy'.
'accepts' means one lot of letters goes inside another.
'military organisation' becomes 'nato'.
'amy' enclosing 'nato' is 'ANATOMY'.
'has' is the link.
(Other definitions for anatomy that I've seen before include "Examining body" , "Study of (physical structure of) living things" , "Study of bodies" , "Study of animal structures" , "Scientific study of bodily structure" .)