my ($re, $fmt) = @ARGV;

function reformat {
    local $_ = $fmt;
    s/%(?:(\d+)|.)/$_[$1] if defined $1/ge;
    return $_;
}

# ...

$re = qr/$re/; # precompile

for(@list_of_files) {
    next unless (my @capture = /$re/);
    rename $_, reformat(@capture);
}