With doxygen you can export your data in html format, tex format, XML (which you can later parse as you want), RTF, Man pages or Docbook.
The html output supports a custom header, footer and stylesheet (CSS) with the HTML_STYLESHEET attribute which might be what you want. You can rewrite those and adjust the output as you like.
If nothing satisfies you, then you might start thinking manually parsing one of the outputs above with your own scripting language and generate the desired format by yourself (if that suits you) or taking over control of the output generation directly via doxygen sources (https://github.com/doxygen/)