This section outlines all the stages in a comprehensive comparative modeling session. In contrast, the tutorial section (Section 1.8) describes a hands-on example illustrating a very simple modeling case. Many ``frequently-asked-questions'' (FAQ) are answered in Section 1.9. An introductory, hands-on primer to comparative modeling with several MODELLER examples can be found in SanSalRev98. With a convenient structure display and manipulation program, it should be possible to do even the difficult modeling cases in only a few days. To find sample script files for all the MODELLER tasks discussed in this section, read file examples/all-steps/README. To obtain additional examples of TOP scripts using a certain command, explore the examples directory, especially the examples/commands sub-directory.