In order to make doxygen use DoxygenFilter please add the following line to your doxygen configuration file (usually doxyfile):
INPUT_FILTER = doxygenfilter
Also, in order to make doxygen include your Perl sources you will want to add "*.pm" and "*.pl" to your FILE_PATTERNS setting.
You will find examples for documented code in the examples directory, either located in the source tree if you downloaded a source package, or in /usr/share/doc/doxygenfilter/examples if you installed a binary package.
Note as of release 1.01 DoxygenFilter now does serious efforts for recognizing classes/methods/functions that are not documented, so that one immediately gets result when running doxygen for the first time even if the code documentation is not yet Doxygen/DoxygenFilter compliant.
The BigSister Network Monitor is written in Perl. It's Doxygen generated code documentation has been put online under code documentation. Note that this project has started using Doxygen lately, so actually most of the documentation is only what Doxygen/DoxygenFilter were able to generate automatically!
The release packages contain a README file and examples, either in the source tree (source package) or installed under /usr/share/doc/doxygenfilter (binary packages).
Please see the Doxygen Web Site to learn how to use doxygen in general.