What is the connection between Lucene and the JSP pages? Are you trying to index the HTML that gets generated by the JSP pages? If so, then check the src/demo directory of the Lucene distribution - it contains an example of how to index HTML. You may wish to substitute a more capable and/or discerning HTML parser like NekoHTML instead of the one used in the example.
If you meant something else, tell us in detail what the problem is.