Can any one please point me in the right direction?

You doesn't need DoxygenFilter to process POD. Also you can use POD to document programs written in languages other than Perl. I always use POD to write documentation for my C projects for example. Looking onto DoxygenFilter own documentation I don't understand why one may choose it as documentation framework. So for me right direction is to use POD (of course that's highly subjective).

You doesn't need DoxygenFilter to process POD

True. I could as well use Pod2html to pretty much achieve that. But I am using Doxygen, because the amount & type of documentation it generates is very useful. Organization by classes, methods, variables, searching etc. It is just way more than POD. But unfortunately Doxygen does not understand POD & that is what DoxygenFilter is trying to address - at least that is what I understood.

After looking onto examples in distribution I have a feeling that DoxygenFilter doesn't support POD. It only adds support for Doxygen style documentation, here's one of the examples:

## @file
# Useful helpers.

## @class
# Container for helper functions.
package Helper;

## @cmethod Helper new()
# Create a new Helper.
sub new {
}

## @fn $ upcase($string)
# Upcase a string.
# @param string a string to be upcased
# @return the upper-case version of string.
sub upcase {
    return uc(shift);
}

1;
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Update: and yes DoxyFilt supports POD, so it seems it's a right tool for you.