This paper presents implementation and pedagogy design of progress-based E-Learning courses with hierarchical subject structures. It extends our previous work on courses with sequential subject structures. The progress-based E-Learning emphasizes personalized course content delivery based on a student?s course comprehension measurement, learning aptitude, and learning progress rules. Supporting courses with hierarchical subject structures increases the range of courses suitable for progress-based E-Learning. It also provides flexibility in course content development. The implementation of these courses can employ the Learning Advancement Management System (LAMS), a Web-based software system we introduced previously for supporting multiple progress-based E-Learning courses through Web services.