Dear Heermann,
I am reactivating this post since we have the similar questions from other users. You can use any python script during the FePEST run for the parameter estimation. Once you create all your PEST files within FePEST, you will see a set of several batch files are also created. There is one in specific named "run_model.bat", where you can place your script line, e.g. python _MyScript.py. The script can run either before or after the FEFLOW run. It is mandatory the script is named with "_" at the beginning to avoid PEST/FePEST deleting the file in between consecutive iterations.
Best,
Carlos