I don't think you need to pass a file handle to the parse_file accessor,passing a filename will do. Then you need to use the links accessor to get all the links in the htm file -

foreach $file (@files) {
    if ($file =~ /^(.*)htm/i){    
        print FileDOut "$file\n";
        my $extor = HTML::SimpleLinkExtor->new();
            $extor->parse_file($file);
        my @all_links   = $extor->links;
            print FileDOut join "\n",@all_links;
    }
}
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