with the hopes that it can help you, I can point to you to the updated lectures on medical applications at the link below. FLUKA and Flair can of course be coupled to anthropomorphic phantoms but the latter are not distributed with the codes so you should import your own.
I suggest you take some acquaintance with the code first and if you need to import your voxel phantom you can have a look at this thread (How to build an anthropomorphic phantom) or similar ones on the forum.
The simulation that you would need for the CNS requires some advanced knowledge/use of the code and I am afraid I cannot give much help with that. Cell lesions that lead to chromosome aberration and are linked to carcinogenesis occur at the cell dimension level. As the article explains, this means in practice that the lesions per cell in a given organ has to be calculated by means of event-by-event track structure simulations at the nm level and then integrated on-line into FLUKA, which adopts a condensed-history approach.
I hope that this proved to be a bit useful.