#!/usr/local/bin/perl
use strict;
use warnings;

if (@ARGV != 3) {
    print "Usage: $0 <pattern file> <input file> <output file>\n";
    exit;
}

my ($pattern_filename, $source_filename, $dest_filename) = @ARGV;

open my $pattern_fh, '<', $pattern_filename or die "Failed to open $pa
+ttern_filename: $!";
my %output_tokens = ();
while (my $line = <$pattern_fh>) {
    chomp $line;
    $output_tokens{$line} = "$line # Added by script";
}

print "Expected tokens: ", join(', ', keys %output_tokens), "\n";

open my $infile, "<",  $source_filename or die "Failed to open $source
+_filename: $!";
open my $outfile,">>", $dest_filename   or die "Failed to open $dest_f
+ilename: $!";

while(my $line = <$infile>) {
    chomp $line;
    $output_tokens{$line} = $line;
}
for my $token (sort keys %output_tokens) {
    print $output_tokens{$token}, "\n";
}

close($infile);
close($outfile);
[download]

Hey

The very first code you provided me with is really working fine for no
+rmal strings without any non-alphabet characters except for its not w
+orking for strings which are like
A[0]
B[1]
So please resolve this .. I tried using the fix you gave but its not w
+orking.So need to modify the code for these cases of strings also.

Rest everything is really fine.
And real thanks for all the innovative solutions you have provided.You
+ really are excellent.
[download]

It seems to work for me, unless I misunderstood your specs. Here are the files I am using:
patterns.txt

A[0]
C
D
[download]

infile.txt

A[0]
B
C
D[0]
D1
DA
[download]

brut.pl

#!/usr/local/bin/perl
use strict;
use warnings;

if (@ARGV != 3) {
    print "Usage: $0 <pattern file> <input file> <output file>\n";
    exit;
}

my ($pattern_filename, $source_filename, $dest_filename) = @ARGV;

open my $pattern_fh, '<', $pattern_filename or die "Failed to open $pa
+ttern_filename: $!";
my @tokens = ();
while (my $line = <$pattern_fh>) {
    chomp $line;
    push @tokens, quotemeta($line);
}
my $pattern = '^(?:' . join('|', @tokens) . ')[^a-zA-Z]*$';
print "Search pattern: $pattern\n";

open my $infile, "<",  $source_filename or die "Failed to open $source
+_filename: $!";
open my $outfile,">>", $dest_filename   or die "Failed to open $dest_f
+ilename: $!";

while(my $line = <$infile>) {
    print "input : $line";
    if ($line =~ /$pattern/) {
        next;
    }
    print "output: $line";
    print $outfile $line;
}
close($infile);
close($outfile);
[download]

perl brut.pl patterns.txt infile.txt outfile.txt

Search pattern: ^(?:A\[0\]|C|D)[^a-zA-Z]*$
input : A[0]
input : B
output: B
input : C
input : D[0]
input : D1
input : DA
output: DA
[download]

1. bin den mig
2. bin
   den
   mig
3. bin deg
   mig

Its as in option 2..that is new line character after each string. I am facing a problem in the code you provided that it is not able to delete strings like bin[0] , bin 12 and bin234. Can you please help on this also.

Ah, you specified that words had to be removed, not tokens that could be part of a word. For the token 'bin' which should be removed:
1. foobin
2. binary
3. bin1
If all of those should be deleted then you can change that pattern from:

my $pattern = '\b(?:' . join('|', @tokens) . ')\b';
[download]

To:

my $pattern = join('|', @tokens);
[download]

If you only want to match words that start with 'bin', and are followed only by non-alpha characters, then this:

my $pattern = '^(?:' . join('|', @tokens) . ')[^a-zA-Z]*$';
[download]

A revised copy that handles the deletion of tokens with a purely line based input:

#!/usr/local/bin/perl
use strict;
use warnings;

if (@ARGV != 3) {
    print "Usage: $0 <pattern file> <input file> <output file>\n";
    exit;
}

my ($pattern_filename, $source_filename, $dest_filename) = @ARGV;

open my $pattern_fh, '<', $pattern_filename or die "Failed to open $pa
+ttern_filename: $!";
my @tokens = ();
while (my $line = <$pattern_fh>) {
    chomp $line;
    push @tokens, $line;
}
my $pattern = '^(?:' . join('|', @tokens) . ')[^a-zA-Z]*$';
print "Search pattern: $pattern\n";

open my $infile, "<",  $source_filename or die "Failed to open $source
+_filename: $!";
open my $outfile,">>", $dest_filename   or die "Failed to open $dest_f
+ilename: $!";

while(my $line = <$infile>) {
    print "input : $line";
    if ($line =~ /$pattern/) {
        next;
    }
    print "output: $line";
    print $outfile $line;
}
close($infile);
close($outfile);
[download]

Its as in option 2 that is new line after every string in both A and B. Also in your code the strings like bin\5\ , bin \43\ and bin\123\ (like array elements with element number in square brackets)are not getting deleted from B. Can you help on this?