There's a few bits of your sample code that don't seem right:

• There's no need to chomp the filename. (harmless though)
• It's odd that you should specify $_ in the pattern match, since you appear to understand how to use it as the default for the split command later. (also harmless)
• Why are you splitting the filename on whitespace? The variable $_ contains only one filename, because the subroutine is being called once for each file. It looks like you think that $_ contains a list of filenames...
• Even so, I don't see why your code wouldn't recurse. It just doesn't do what you want.

Your test sub could be written more simply:

sub get_good_int {
  next if /^unknown/;
  print "My filename is: $_\n";
}
[download]

Something closer to being useful might be this:

use File::Find;
use File::Basename;

find (\get_good_int, '/nfs/export/netflow/intermediate');

sub get_good_int {
  next if /^unknown/;
  
  # If the directory path includes this type of dir
  if ($File::Find::dir =~ m#/questionable-\d{6}-\d{6}#) {
    myfunc1($_);
  }
  # If it contains this other type of dir
  elsif ($File::Find::dir =~ m#/\d{6}-\d{6}#) {
    myfunc2($_);
  }
}
[download]

buckaduck