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.
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.
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Want more info? How to link or
or How to display code and escape characters
are good places to start.