For anyone out there who uses the free mbsystem multibeam processing software (developed by Dave Caress at the Monterey Bay Aquarium Research Institute (MBARI)) and has also got Fledermaus version 7 then in the upcoming 7.1 release you can now take the mbsystem fbt files and clean them or grid them in Fledermaus. This will allow you to use the CUBE algorithm to speed up your processing. Once you have finished your data cleaning/processing in Fledermaus you can unload the changes back to the fbt files and use these within mbsystem or GMT as you do currently. The files seems to load really quickly and that is both for creating DTMs and also for creating the PFM data structure which Fledermaus uses to process the data.
Here are some screen captures showing the lines and a grid in 2D in DMagic and then the PFM loaded into Fledermaus. Lastly a point cloud view coloured by line in the 3DEditor where you can reject bad points.