Is there a way to create a console application which is not visible on the normal desktop as well as on task bar.I want to create an application which runs just as the system processes,they can be seen only in task manager.
It's not really a console application then, right? If you have a WinMain() instead of a main(), I think nothing should be created. I don't know about linux. Also, any GUI toolkit should do this if you don't explicitly tell it to create a window.
Daemons (system modules) and/or system services (in Windows world) would be more suited in this case rather than a GUI application. A GUI application that does not show anything is just unnecessarily complex for both code (you have to build with libraries you don't need) and program (loading/using libraries it does not really need).