I'm a little confused. What does a directory have to do with searching? You can certainly build the *index* from files in a directory, but Lucene doesn't search files themselves, it searches the *index* built from the files.
If I'm interpreting your problem correctly, you'll have to build an index, perhaps putting some designator in each document about where it came from. Crudely, you could just store the file path that the file was indexed from, or even just some designation. For instance, a field "origin", with values "mother", "father", "son", "daughter". Then your search could restrict itself to documents with the "origin" field however you choose. Hope that helps Erick