In general it would be a good idea that calibre does not use the internal viewer for those formats -- PDF conversion is horrible and Word is superior than ebook-viewer for DOC/X. In fact, that (unchecked) is the default.
As BetterRed said -- just open the format in your OS-default application, it probably has some builtin way of doing what you need.
PDF and DOCX should be fine -- but not EPUB or other standard
ebook formats, since they don't have standards for embedded annotations. But that may not be necessary -- you only mentioned PDF and DOCX. Just thought I'd mention it to cover all the bases.