Hello @parveez,
I had a look on your model and there are multiple reasons for its behaviour.
If I understand correctly, you want to connect with FreeMaster over the USB cable/Serial connection and to transfer messages over CAN bus.
If so, this is what I've found in the attached model.
1. FreeMaster setup: Razvan mentioned above the pins required for the connection. For the FreeMaster you have selected other pins that the ones connected to OpenSDA.

2. The FCAN_Receive block makes some settings in the step function, configuring the RX message buffer. And in the model that you send, the code generated by the Receive block was inserted before the FCAN Configuration code, which means that the board was ending up running a dummy handler. To set the execution order for some important blocks, like the Config, Send and Receive, you can right click on the block, open the Properties and insert a priority.

Finally the execution order looks like this: First is the FCAN COnfig, then the Transmit and then the receive.

Last but not least, are you powering the board externally using the J16 connector? because as far as I know, in order to use the CAN transciever, you need to power the board using the external supply.
I can't test the communication because I don't have for now a CAN analyzer but the FreeMaster over USB works.
Hope this helps,
Marius