There isn't just one way of doing it.
Apart from exporting to Excel as suggested by Pete you could also export the process variables (e.g. temperatures) as a shapefile and make field calculations using GIS. In addition, the FEFLOW Support provides a plugin, which calculates the minimum, the maximum and the mean temperature after each time-step of a transient model.
If you are interested please contact the FEFLOW support: http://www.mikepoweredbydhi.com/support.