Hey Chrisoula,
as Eladd already pointed out, in version 5.2 it's a little more complicated.
The traditional way is to define observation points for your model slices (see "Info - Help - Glossary - R - Reference Distributions - Reference Data - Observation single points" for details). FeFlow will write the simulated heads for those observation points to the DAR file. The DAR file is a simple text file and you can find those exported heads at the end of the file. Copy-and-Pasting them to Excel is one option to compare them to your observed values.
All this can be automated using IFM modules, but that requires programming skills. All you need then is an input file with your observation point locations. The IFM module would read that file and write the data plus simulated heads to an output file.
At the FeFlow User Conference in Berlin last year, I gave a presentation about this and attach the paper that came with it for your information.
Good luck, Chris