MB-System™ rides atop a library of functions for reading and writing swath mapping sonar data files called MBIO,(Multi Beam Input-Output).While largely unseen by the user, MBIO is where the rubber meets the road. MBIO takes into account multitudes of details, including existence of side scan or and or amplitude data, interpolation of navigation to ping times, geometry of specific sonar models, and of course the various data formats themselves. While MBIO does not support every possible data type, it has grown to accommodate the bulk of the sonar data formats common the the multibeam community. Indeed, considerable development is ongoing to support ever greater variations in sonar data formats, created both by commercial vendors and research institutions.

In addition to the native data formats, MBIO defines many MB-System™-only data formats. These have been created out of necessity when vendor native formats fail to accommodate the needs required of sonar processing, or are too unwieldy to store. For example, some Simrad sonars have traditionally stored navigation information separate from the bathymetry information, requiring interpolation of navigation to ping times each time the data is read. MBIO defines a data format stores the bathymetry and the interpolated navigation in a single composite file. Similarly, native Hydrosweep DS-2 data contain no less than 9 separate data files with multitudes of ancillary information regarding the sonar's settings, but far more information than the sonar data itself. In this case, MBIO defines an alternate format that condenses the necessary navigation, bathymetry and sidescan information into a single, more manageable and considerably smaller file. Many research institutions have found the MB-System™ formats preferable to the native sonar formats and perform a real time conversion of sonar data for their users.

Stating which sonar and sonar formats are supported by MB-System™ is something of a moving target, however as of the time of this writing the following sonars were supported: