Thanks Peter for the response...
After posting, I saw inadvertently a thread that explained this, I gave it a try, but still got the same issues you see in that elements of the internal partitions still poke up through the roof.
The roof is rather messy, after I turned it from a mesh to a roof, underneath isn't continuous at all, it is very segmented, I think this may be part of the problem....Any advice on tidying up the roof?
See pic of underneath the roof..
Cheers again for all help...