I've found a
Word filter from Microsoft that is supposed to output cleaner HTML. (I assume this is what you were talking about.)
I also tend to use Dreamweaver for this task, but it does leave some of the CSS stuff behind, so some cleanup is still required.
Update: Although I still haven't tested the output, it appears that the MS Word filter can be used from the
command line, as a standalone GUI application, or from within Word, and can batch process multiple files.
Impossible Robot