Have you tried looking at the documentation on CPAN for this? http://search.cpan.org/~jordan/Doxygen-Filter-Perl-1.00/lib/Doxygen/Filter/Perl.pm Have you asked this question on the Doxygen::Filter::Perl discussions board on SF?

There are few things you need to do to make this work.

• You need to have Doxygen installed on your computer. And you need to have the doxygen command in your path. I am guessing in Windows land this would be doxygen.exe
• You need a Doxyfile configuration file for your project or script. This basically tells Doxygen what to do, where to find files, and where to put the html output. I would suggest using the Doxyfile example that is included in Doxygen::Filter::Perl. The CPAN docs explain the two options that needs to be changed.
• There is a perl script called doxygen-filter-perl not to be confused with Doxygen::Filter::Perl that Doxygen will call to figure out which files to pre-filter. This script will look for files with a .pl or .pm. You can changes this how ever you need. On Windows you will also probably need to make sure the Doxyfile configuration file points to where ever you have doxygen-filter-perl installed.

Then all you need to do is run "doxygen.exe Doxyfile" and it will generate some html output for you. The CPAN docs say that what this does is generate C like documentation out of the perl code/model so that doxygen can understand it. Thus a "use" command is turned in to a #include. This will make all of the inheritance diagrams work right and do some pretty cool things for documenting your perl code.

As far as documenting a subroutine, once again, look at the Docs on CPAN.

#** @function public subnamedfoo ($var, $foo, $bar)
# This function subnamedfoo does XYZ
# and it does some more of this and that
# @params var required this value is for xyz
# @params foo required this value is for abc
# @params bar optional this is not really needed for xyz
# @retval retval this is a string that does bla
#*
sub subnamedfoo {
my $var = shift;
my $foo = shift;
my $bar = shift;
#..... do something ......
return $retval;
}