We are now almost ready to run MT3DMS. The one thing we have to do first is to run MODFLOW again. When MODFLOW is run this time, it will create a flow-transport link file. MT3DMS uses this file as part of its input. To run MODFLOW, select File|Export|MODFLOW Input Files or click the Run MODFLOW button 
and save the MODFLOW input files. When MODFLOW has finished running, select File|Export|MT3DMS Input Files or click the down arrow next to the Run MODFLOW button and select Export MT3DMS Input Files.
