Web usage mining (WUM) is the process of extracting navigation behaviour patterns that allow analysing users' interactions with Web-based environments. We discuss the impact of developing the WUM preprocessing phase according to concepts, problems and goals specific to Web-based learning environments. We present a tool prototype that automates typical tasks performed in the pre-processing phase, by offering operators that implement these tasks. The tool seeks for the active involvement of domain-related people (e.g. instructors). Functionality makes easier the alignment of mining goals with required pre-processing tasks, by addressing the configuration of operators visually and by enabling the reuse of existing configurations.