Right now I am working on developing a standalone application in C++ using libraries of cpp-ethereum, I was looking at the source code for cpp-ethereum and an idea stuck into my mind that wouldn't it be cool if we can use whisper protocol of cpp-ethereum for transferring actual data like actual file transfer? Can we do it?
No. Of course it's possible what you suggesting, but no, because you have a major mixup in terminology.
For a peer 2 peer communication layer, have a look at devp2p. Here is the specification.
Whisper is a peer 2 peer encrypted messanging protocol, currently pushed by status.im, the latest spec is here. As far as I know is only geth featuring a pretty current implementation, no idea about the C++ status.
In general, just a heads up, the C++ client is deprecated for production use. If you are interested in further developing against swarm or whisper, take a look into go-ethereum. Or contribute to cpp-ethereum.