Can't do. You don't mix folders and files which is what it sounds like you are doing.
for example
top folder called Shared has list for everyone does not contain files
subfolders by dept shared only to that dept. That top folder can contain files as long as you don't want to do denied in subfolders below it.
You can use deny but you have to stop inheritance at that point and deny's can get messy. Try to avoid using deny.