@ngunathilake and @DaneW I was able to follow @ggiraldof 's suggestion on performing “Union” operation within SimScale’s CAD mode for most of the parts. Although the diffusers are not properly connected to the ducts, which prevents us to get a single fluid volume .
Simple solution would be to extend the pipe sections to interfere with the diffusers and then perform boolean → Union operation again to correct the model. Once done, you would be able to use the CAD model for the simulation.
Please refer to this Tutorial on “CAD Cleaning of a pipe Geometry” to understand the requirements.