Empty box protecting organ (5,3)
I believe the answer is:
clear out
'empty' is the definition.
(clearing out is a kind of emptying)
'box protecting organ' is the wordplay.
'box' becomes 'clout' (I've seen this before).
'protecting' means one lot of letters goes inside another (inserted letters are held or protected).
'organ' becomes 'ear' (the ear is an organ).
'clout' placed around 'ear' is 'CLEAR OUT'.
(Other definitions for clear out that I've seen before include "Get rid of" , "Leave quickly" , "Empty" .)