Hi Rakesh,
I don't think you can fully operate Clarizen in a frame inside your application. For a start, many of the links target the top frame.
You can, however, embed specific views (particularly ones shared with read only option) in your application.
Running in iFrame is a potential security risk, so it is blocked by default.
You can allow embedding by checking system setting 3.9 'Enable Clarizen page embedding'.
Hope this helps,
Ophir