Rendering windows having transparent properties from a remote desktop environment

Embodiments of the present disclosure relate to a remote desktop system which allows an application that executes on a remote computing device to be presented to a remote terminal as if the application is executing on the remote terminal. This system determines which of the remote computing device's application windows are top-level windows, and creates a rendering target for each top-level window. The rendering target is a graphics surface that is marshaled to the remote terminal. A PDU (Protocol Data Channel) is produced over this first graphics surface that includes a mapping of the location of the top-level window. A second graphics surface containing transparency information is created for a top-level window that contains a transparency characteristic. This second graphics surface is encoded and marshaled to the remote terminal separately from the first graphics surface. The client computing device receives and merges the two graphics surfaces, and renders a window with the expected transparency.