DDSCAT can work with complex structures. DDSCAT will calculate Muller matrix elements for the far-field, and can also do near-field calculations if desired. However, if the desired target geometry isn't one of the built-in target options, you will need to either (1) modify DDSCAT or (2) generate the list of "occupied" lattice sites (and compositions) using your own software tools, and use the FROM_FILE target option in DDSCAT to read in the list of occcupied sites. Option (2) is generally simplest since is doesn't require andy changes to DDSCAT.
The UserGuide describes how the input file for target option FROM_FILE should be formatted. There is a sample calculation in the examples/FROM_FILE directory.
Keep in mind that if one has a multilayer target, the interdipole spacing d should be small enough to resolve the thickness of the thinnest layer. One should always do a "resolution study" to verify that your results are not sensitive to your choice of interdipole spacing d.
