Didn't find much in the way of Perl modules for working with MS Word files.

Depending on just what needs to be done, maybe you could extract text from the document with Text::Extract::Word, edit the resulting text, then convert the text to HTML using HTML::FromText, saving the resulting HTML with a .doc extension. MS Word will read that without complaint.* Of course, the original formatting will be lost. (Though any formatting your Perl program puts in the HTML will be accepted by MS Word.)

(There is Win32::Word::Writer, but it would be harder to use than what I suggested, above.)

Alternately, there are tools for converting docx files to ODF files and several Perl modules for working with ODF files. Then your program can modify it and MSWord can read the result. (Supposedly, MSWord can also export to ODF - assuming you can convince your users to do that.)

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* I know this because, when I had a website, resume.doc was just a symbolic link to resume.html