In a pen-based computing system, a user-specific smart pen application is created from a template application using customer authoring tools. The template application contains computer program code that is to be executed by a processor of a smart pen. Application content and a representation for printed content are received. The application content, provided by user or customer, defines functional interactions between the printed content representation and a smart pen. The template application is combined with application content to generate a user-specific application comprising instructions for being executed on a processor of a smart pen. The user-specific application is stored on a storage medium.