use strict;
use warnings;

use Time::Local ();

my $file_name = shift(@ARGV);

open(LOG_FH, '<', $file_name)
or die("...$/");

open(TMP_FH, '>', $file_name.'.tmp')
or die("...$/");

# Might want to clear the hours, minutes and secs from $old.
my $old = time - 90*24*60*60;

while (<LOG_FH>) {
   my ($y, $m, $d) = /...(...)...(...)...(...).../;
   my $date = Time::Local::timelocal(0, 0, 0, $d, $m-1, $y);
   last if $date > $old;
}

do {
   print TMP_FH $_;
} while (<LOG_FH>);

close(LOG_FH);
close(TMP_FH);

unlink($file_name);
rename($file_name.'.tmp', $file_name);
[download]

Replace ...s with appropriate code. Off the top of my head. There may be a better way. Doesn't lock. Untested.

Actually, Forget everything I said and run Logfile::Rotate as a cron job every 90 days.

Update: I forgot that you specified the date format. Time::ParseDate would probably be of more use than Time::Local.