Instrument prodding trooper's cheeks (6)
I believe the answer is:
glutei
'cheeks' is the definition.
(buttock muscles)
'instrument prodding trooper's' is the wordplay.
'instrument' becomes 'lute' (lute is a kind of instrument).
'prodding' indicates putting letters inside (prod can mean to poke a hole into something).
'trooper' becomes 'gi' (term for US soldier).
'lute' going within 'gi' is 'GLUTEI'.
(Other definitions for glutei that I've seen before include "behind?" , "muscles" .)