You can only index whole folders, skipping some subfolders (at any depth) you manually add to the relevant pane.
However, there is a hidden preference (configurable from Terminal.app) to exclude files or entire folders based on their name or path. This won't work for Finder tags, but might work for pseudo-tags you add to file or folder names (e.g.: "Thesis [lin-alg].pdf".
See "Skipping some folders at indexing time" in our hidden Preferences documentation