Look at the what differentiates each windows. Try to use object spy on each window and see whats unique and reusable about them, this is often the title (text property), index, style, object class, hwnd id, often the focus shift to the new window so you can use the focus property. Then, since these are dynamic windows you will probably have to write your test using descriptive programming.

The problem is each window, pops up several windows within it. when I say pops up, I mean on click of every button in that particular window. so I'm finding it difficult to capture all the objects pertaining to an action. Is it better to capture each window as an action?