I can't tell, whether my correction will give you the desired result - NO - I'm SURE they won't - but maybe it gives you an idea where you lack knowledge.

open(STDIN1, "<icd_meas_child.txt")
#  --NO--              or die "Cannot open file";
                or die "Cannot open icd_meas_child.txt: $!\n";
                # Don't leave people unsure about which file and what 
+reason ($!)
            @row1 = <STDIN1>;

            # What do you think you're doing here?
            # for (@row1[$done1])
            # try
            foreach (@row)
                 {
                 # OUCH! Don't chop if you want to chomp!
                 # chop(@row1);
                   chomp;
                   # And what do you think will this do?
                   # foreach (@row1[$count1])
                   # {
                   #   @column1 = split(/\,/,@row1[$count1]);
                   #    $sat_name      = @column1[0];
                   #    $meas_name     = @column1[1];
                   #    $parent_meas   = @column1[2];
                   #    $start_bit_no  = @column1[3];
                   ($sat_name, $meas_name, $parent_meas, $start_bit_no
+)= split /,/;
                       print ("$sat_name;");
                       print ("$meas_name;");
                   &DESCRIPTION; # <---- What do these do?
                   &DATA;        # <--/
                       print ("$size_bits_no;");
                       &DATA1;   # ???
                       print ("$monitor_type;");
                       print ("$parent_meas;");
                       &BIT;
                       print ("$start_bit_no;");
                       &SUBSYSTEM;   # ???
                       &BOX;   # ???
                       print ("$lsb_proc_ind;");
                       print ("$blank");
                       print ("\n");
                       $count1++;
                   # }

                 $done1++;
                 }
close STDIN1;


sub BIT #routine to sort numbers
{
# OUCH! You know what you do???
# if ($meas_name = $parent_meas)
# I think you meant
if ($meas_name == $parent_meas)
  {
    # I won't even try to imagine what this line WILL do
    # my @nums = $start_bit_no;
    # I think it SHOULD do
    push(@nums, $start_bit_no);
    # So pushing the start bit to a global array
    my @index= sort { $nums[$a-1] <=> $nums[$b-1] } 1..@nums;
    # Fortunately you mad the following line a comment by a typo ;-)
    #$index++;
    # But here OUCH again
    #print join "\n","@index;",'';
    # Are you sure you didn't mean:
    print join("\n",@index),"\n";
  }

}
__END__
A1,BL1CHILDB0,BL1PARENTMON,0
A1,BL1CHILDB1,BL1PARENTMON,1
A1,BL1CHILDB2,BL1PARENTMON,2
A1,BL1CHILDB3,BL1PARENTMON,3
A1,BL1CHILDB4,BL1PARENTMON,4
A1,BL2CHILDB5,BL1PARENTMON,5
A1,BL2CHILDB6,BL1PARENTMON,6
A1,BL2CHILDB7,BL1PARENTMON,7
A1,BL2CHILDB3,BL2PARENTMON,1
A1,BL2CHILDB6,BL2PARENTMON,0
A1,D1CHILDB0,D1PARENTMON,0
A1,D2CHILDB1T3,D1PARENTMON,1
A1,D3CHILDB4T5,D1PARENTMON,4
A1,D4CHILDB6,D1PARENTMON,6
A1,D5CHILDB7,D1PARENTMON,7
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