Hello Simona,
The way OptiFDTD evaluates far field is that the simulation models the optical system and can store the DFT of the field using observation lines/areas. This data can then be used in a far field utility to project the field out to a given distance.
Depending on the configuration you could try and run 3 simulations. One to setup the source and project it to the far field. The second using that one as a source and model your tissue interaction. Then a third to project those results to a far field observer.
Are you able to provide us with a few more details regarding the overall geometry of your system?
Once we can sort out a possible solution, there is a 30-day evaluation for you to try out and see if the solution works for your application.,
Scott