#opening the file for reading
  open IN,"$fileName" ;
  #reading the whole file into an array.
  my @F=<IN>; 
  close IN;
  #reading the last line of the file
  my $lastLine=$F[$#F];
  my $firstLine=$F[0];

  #spliting last line by tabs
  my @line=split /\t/,$lastLine;
  #spliting first line by tabs
  my @firstSplitLine=split /\t/,$firstLine;
  #finding the column number that equals the fieldName
  my $fieldNum = -1;
  my $numberOfFields = scalar(@firstSplitLine);
  for($counter=0 ; $counter < $numberOfFields ; $counter++)
  {
    $ourstring = $firstSplitLine[$counter];
    $ourstring =~ s/\n\n/\n/g; #=~ s/ \s//g;# HERE IS WHERE I'M TRYING
+ DIFFERENT STUFF...
     if($fieldName eq $ourstring) # The "problematic" area
     {
    $fieldNum=$counter;
    last;
     }
  }
  # if the field wasn't found
  if($fieldNum==-1)
  {
  print STDERR "\n" if ($permit_writing);
  print STDERR "The field you asked for was not found, now returning l
+ast value: $lastValue\n" if ($permit_writing);
  print STDERR "\n" if ($permit_writing);
  return $lastValue;
  }
  #printing the required field
  print STDERR "    Value: $line[$fieldNum]\n\n" if ($permit_writing);
  return $line[$fieldNum];
[download]

Edit: Changed <pre> tags to <code> tags (davorg)

(Please use <code> tags to display code, not <pre>tags)

Do you have "use warnings" in your code? I ask because the important piece of your code seems to be if($fieldName eq $ourstring) and according to the extract you've shown us, $fieldName is undefined at that point.

But assuming that it's set somewhere outside of this extract, I still think that you can simplify a lot of this code. I'd consider setting up a hash where the keys are the column names and the associated values are the column numbers. Something like:

my %columns;
@columns{@split_first_line} = 0 .. $#split_first_line;
[download]

You can then get the column number associated with a given field name with a simple:

if (defined (my $field_num = $columns{$field_name})) {
  # field exists
}
[download]

Also, the best place to deal with chomping the input data is probably as soon as you've read it in, when a simple chomp(@f) would suffice.

--
<http://dave.org.uk>

"The first rule of Perl club is you do not talk about Perl club."
-- Chip Salzenberg