Details on how to set up a 3D frame can be found in the MasterFrame manual, including setting the floor beams to be of composite construction. See the MasterFrame Manual, chapter 'Creating a Model'. Details on composite construction are found at Levels, Loading and Construction Defaults.
The default construction type (composite) and applied loads (dead and live) are set up for each floor in the model using the Default Levels panel.
Area loading panels are assigned to the floors and roofs - see Floor and Roof Panels - Area Loading and Construction (Pro) and Area Loading.
You can view which beams are being seen as composite by the program. Click on the 3D icon and the option to Colour by Material. The frame elements are coloured by material, for example, steel elements are shown in green, composite members in yellow, bracing members in blue, timber in brown and concrete in grey.
Steel & composite beams definitions can be set up - see Composite Beam to Slab Construction Type Member Groups (Pro). These will allow beams that are to be non-composite to be set as such in an overall composite floor, eg, trimmer beams, etc.
Design groups can also be set up - see Steel and Composite Member Design Groups (Pro). This enables groups of beams which will have the same data to be grouped together so that if that data on one beam is altered, then the whole group is altered.
Note that in a MasterFrame composite model the first 5 loadcases are automatically set up to include the Ultimate Limit State (Final Stage), Ultimate Limit State (Construction Stage), Live (Serviceability), Super Imposed Dead (Serviceability) and Dead (Serviceability) load combinations. These are required so that the composite design of the beams can be carried out later. If you delete or modify these cases, they will be automatically restored prior to analysis.