What you can do to fix it, for starters, is stop putting shared functionality in a .pl file. It's a lot less confusing if you follow convention. Further to that convention is to put your shared code in its own package. And if you want to export it to the caller's namespace, check Exporter (or any number of similar modules, such as Perl6::Export::Attrs).

What's happening is that inside Modis/ParseMe.pm, you require the file. The subs.pl file gets loaded, everything gets inserted into your Modis::ParseMe namespace (since that's the package in effect when subs.pl is loaded). Then, back in main, you require it again. However, perl sees that it's already loaded, and doesn't reload it. Thus no functions are inserted into the main namespace (package).

If you put them into an exportable namespace and use the module, both places can use it, and both places will work.

Technically, if you put a package at the top of subs.pl, that should work, but you're going against convention. I'd encourage you to go with a module instead.