Top student indicates that is not applicable in Italian city (5)
I believe the answer is:
siena
'italian city' is the definition.
(Siena is a city in Italy)
'top student indicates that is not applicable' is the wordplay.
'top' indicates taking the first letters (in a down clue, the first letter is top).
'that is not applicable' becomes 'ena' (I can't justify this - if you can you should believe this answer much more).
The initial letters of 'student indicates' is 'si'.
'si'+'ena'='SIENA'
'in' acts as a link.
Can you help me to learn more?
(Other definitions for siena that I've seen before include "city in Italy" , "somewhere in Italy)" , "City of St Catherine in Tuscany" , "Tuscan town" , "Italian city strangely in sea" .)