Hi,
I am using windows command window to run pre_aem3d to generate the files. I would edit all the necessary files in the Bathymetry folder. Edit the run_pre.dat file for paths linked to their input and output locations. Note that unf files goes to the "infiles" folder within the "run" folder and the paths in the "run_pre.dat" file should point to the right locations. Finally, change your command window path to your "pre" folder and then execute the command: pre_aem3d The pre-processor will print out the status of the process to the command window or the debug_pre.txt file.
Good luck
Seyoum