Sketching in 3D is a useful way to access knowledge-based design systems. In this paper we present a framework for sketch-based interaction with intelligent systems in three dimensional domains. The Space Pen software written in Java 3D is used as a platform to implement two architectural lighting design tools. Space Pen supports user annotations in the form of sketching, virtual post-it notes, and sketch object insertions. Spot supports access to direct sunlight simulation and visualization in a selected time period with sketching in 3D space. Light Pen suggests placement of lamps to light an intended area in space. In these examples, the 3D sketching front-end serves as an interface to a back end knowledge-based system. The designer can pose problems by drawing onto a 3D model to which the knowledge-based systems offer a solution by either providing quantitative data analysis or modifying the 3-D model. The specific domain of architectural lighting is implemented, it exemplifies a more general class of 3-D pen-based interaction with intelligent systems.