open my $INFILE, '<', 'myfile';
my $number = 0;

while ($INFILE){
  $_ =~ m/\#RD\#(.*?)\#OE\#/;
  my $number++;
  open my $OUTFILE, '>', "outfile$number";
  print $OUTFILE $1;
  close $OUTFILE;
}
close $INFILE;