Sausage trimmed in small rooms in Manhattan home (3,6)
I believe the answer is:
los alamos
'manhattan home' is the definition.
(home of the Manhattan nuclear project)
'sausage trimmed in small rooms in' is the wordplay.
'sausage' becomes 'salami' (salami is a kind of sausage).
'trimmed' means to remove the last letter (the final letter is trimmed off).
'in small rooms' becomes 'loos' (I can't explain this - if you can you should give a lot more credence to this answer).
'in' is an insertion indicator.
'salami' with its last letter removed is 'salam'.
'salam' put inside 'loos' is 'LOS ALAMOS'.
(Another definition for los alamos that I've seen is " research centre".)