You'll find this more reliable

sub dequote {
   local *_ = \$_[0];
   s/^"(.*)"$/$1/;
   s/\\(.)/$1/g;
}


      if ($line =~ m/
        -([^\S"\\]+)           # An dashed identifier
        (?:                    # optionally followed by
          \s+                  # whitespace
          (                    # and either
            "(?:[^"\\]|\\.)*"  # a quoted string
            |                  # or
            [^\S"\\]+          # a bare identifer.
          )
        )?
      /x)
      {
         my ($opt, $arg) = ($1, $2);
         dequote($arg);
         $DATAFROMBATCHFILE[$counter]{$opt} = $arg;
      }
      elsif ($line =~ m/\bEND\b/)
      {
         $counter ++;
      }
[download]

You're using a hash as an array again. Are you used to programming in PHP? I fixed it to use an array (meaning I changed {} to []. If the key to a hash is a number, chances are you should be using an array.

#1

Please comment your code, then it would be easier to know what it is supposed to do (as opposed to what it actually does)

I'm not sure what it is you are doing with HASHDATAFROMBATCHFILE, but I will ignore that for now.

#2

what's wrong with the quotes extraction since i don't want them there.

My source code (same as yours, but reads input from __DATA__, and deleted the unused hash)

#!/usr/bin/perl -w
use strict;
my $counter;
while (my $line = <DATA>)
   {
      chomp($line);
      print "B |$line|\n";
      if ($line =~ m/-(.*) ["]*([\)\(A-Za-z0-9,\.\*]*)\s*["]*\s*/)
      {
         print "$counter $1 $2\n";
      }
      if ($line =~ m/\bEND\b/)
      {
         $counter ++;
      }
   }

__DATA__
   -libs "source*.lib"
   -1dlu 
   -2dlu 
   -3dlu "(1,1,3)"
   -filter  ASDF
END
[download]

B |   -libs "source*.lib"|
 libs source*.lib
B |   -1dlu |
 1dlu 
B |   -2dlu |
 2dlu 
B |   -3dlu "(1,1,3)"|
 3dlu (1,1,3)
B |   -filter  ASDF|
 filter  ASDF
B |END|
[download]

#!/usr/bin/perl -w
use strict;

while (<DATA>) {
    chomp;
    print "$_\n";

    if (/-(\S+)(\s*(.*))?/x) {
        my ($p1, $p2) = ($1, $3);
        if (defined $p2) {
            $p2 =~ s/^"//; $p2 =~ s/"$//;
        }
        print "[$p1][$p2]\n";
    }
}



__DATA__
   -libs "source*.lib source*.lib"
   -1dlu
   -2dlu
   -3dlu "(1,1,3)"
   -filter  ASDF
[download]