Get Application's Window Handles

You could do what Process.MainWindowHandle appears to do: use P/Invoke to call the EnumWindows function, which invokes a callback method for every top-level window in the system.

In your callback, call GetWindowThreadProcessId, and compare the window's process id with Process.Id; if the process ids match, add the window handle to a list.

First, you'll have to get the windowhandle of the application's mainwindow.

 [DllImport("user32.dll", SetLastError = true)]
 static extern IntPtr FindWindow(string lpClassName, string lpWindowName);

 IntPtr hWnd = (IntPtr)FindWindow(windowName, null);

Then, you can use this handle to get all childwindows:

[DllImport("user32.dll")]
[return: MarshalAs(UnmanagedType.Bool)]
static extern bool EnumChildWindows(IntPtr hwndParent, EnumWindowsProc lpEnumFunc, IntPtr lParam);

private List<IntPtr> GetChildWindows(IntPtr parent)  
{  
    List<IntPtr> result = new List<IntPtr>();  
    GCHandle listHandle = GCHandle.Alloc(result);  
    try  
    {  
         EnumWindowProc childProc = new EnumWindowProc(EnumWindow);  
         EnumChildWindows(parent, childProc, GCHandle.ToIntPtr(listHandle));  
    }  
    finally  
    {  
         if (listHandle.IsAllocated)  
               listHandle.Free();  
    }  
    return result;  
}