What have you tried so far?

When you read an empty line, you can't know yet whether to print it. So you need something along the lines of

my $newlines = 0;
while (<$file>) {
    if (/^$/) {
        $newlines++;
    }
    else {
        print "\n" x $newlines;
        print;
        $newlines = 0;
    }
}
[download]

(untestested).

update: closed regex, ww++.