my $ennumerate=0;

...

#you probably have a loop like this in your script?
while ($line=<$fh>) {

#insert this into the loop:
  if ($ennumerate==1) {
    if ($line=~/^#(.*)/) {
      print "\\item $1\n";
    }
    else {
      $ennumerate=0;
      print "\\end{enumerate}\n";
  }
  else {
    if ($line=~/^#(.*)/) {
       print "\\begin{enumerate}\n";
       print "\\item $1";
       $ennumerate=1;
    }
  }

...
}