Hi Amol,
Sorry for the delay. If I am reading your requirement right, in your case, you should be able to add the application within the folder and then be sure to right-click on the application and set it to "Set Visible as a Quicklink". You can even use personalization to disable to folder, so the user won't click on the folder, but instead they can click the Quicklink to go directly to the application.
Let me know if that is not the case.
Thanks,
-Kevin