foreach my $dir (@directories)
{
    foreach my $file (@filenames)
    {
        $age = -M $file;
    ....

##</code><code>##

foreach my $dir (@directories)
{
    foreach my $file (@filenames)
    {
        $age = -M "$dir/$file";  # see the difference?
    ....

##</code><code>##

foreach my $dir (@directories)
{
    chdir $dir or die "Couldn't chdir to $dir: $!\n";
    foreach my $file (@filenames)
    {
        $age = -M $file;
        ....
    }
    chdir ".." or die "Help, I stranded myself";