Top part of church lacking second cross (4)
I believe the answer is:
apex
'top' is the definition.
(apex is a top or peak)
'part of church lacking second cross' is the wordplay.
'part of church' becomes 'apse' (part of a church building).
'lacking' indicates named letters should be taken away.
'second' becomes 's' (common abbreviation).
'cross' becomes 'x' (an X is a cross).
'apse' with 's' removed is 'ape'.
'ape'+'x'='APEX'
(Other definitions for apex that I've seen before include "reasonable fare" , "Apogee, summit" , "Peak, vertex" , "white collar union" , "Pointed top" .)