use strict;
use warnings;
my $file1 = 'C:/Users/Siddharth/Desktop/goodfile.txt'; 
my $file2 = 'C:/Users/Siddharth/Desktop/badfile.txt'; 
 
open my  $h2, '<', $file2 or die "cannot open file2";


my @a2 = <$h2>;
close $h2;
chomp @a2;
my $match = join '|', @a2;
$match = qr/$match/;

open my $f3,'>',"C:/Users/Siddharth/Desktop/do.txt" or die "$!";
open my $h1, '<', $file1 or die "cannot open file1";
my @a1 = <$h1>;
close $h1;
#my $fh = grep {$_ !~ $match} @a1;
#print $f3 $fh;
print grep {$_ !~ $match} @a1;
[download]

If I have the input files
file1.txt:

1.he is man
2.don't you
3.xyzzy
4.what goes on
[download]

and
file2.txt:

he is
z
what are
try to do
[download]

and I run the script
pm_11118096_1.pl:

# pm_11118096_1.pl                                          15jun20waw

use strict;
use warnings;

my $file1 = 'file1.txt';
my $file2 = 'file2.txt';

open my  $h2, '<', $file2 or die "cannot open file2";

my @a2 = <$h2>;
close $h2;
chomp @a2;
my $match = join '|', @a2;
$match = qr/$match/;

open my $f3,'>',"do.txt" or die "$!";
open my $h1, '<', $file1 or die "cannot open file1";
my @a1 = <$h1>;
close $h1;

print grep {$_ !~ $match} @a1;
# print $f3 grep {$_ !~ $match} @a1;
[download]

I get the following output:

c:\@Work\Perl\monks\Sidd@786>perl pm_11118096_1.pl
2.don't you
4.what goes on
[download]

If I comment out the
    # print grep {$_ !~ $match} @a1;
line and uncomment the
    print $f3 grep {$_ !~ $match} @a1;
line, I get an output file do.txt with the content

2.don't you
4.what goes on
[download]

(and no output in the command window).

When you run your code with these input files, what do you get?

---

Give a man a fish:  <%-{-{-{-<

it is again printing nothing

Perhaps your algorithm is wrong or perhaps your data isn't what you think it is. Here is an SSCCE:

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

my @a2 = qw/foo bar baz/;
my $match = join '|', @a2;
my @a1 = qw/bar quux/;
print grep {$_ !~ $match} @a1;
[download]

This prints one blank line (for "bar") and one line with "quux" in it. Do you understand why?

Amended thanks to AnomalousMonk for pointing out the error.

    #use strict;
use warnings;

 $file1 = 'C:/Users/Siddharth/Desktop/our.txt';
 $file2 = 'C:/Users/Siddharth/Desktop/my.txt';

open  $h2, '<', $file2 or die "cannot open file2";

 @a2 = <$h2>;
close $h2;
chomp @a2;
 $match = join '|', @a2;
$match = qr/$match/;

open  $f3,'>',"C:/Users/Siddharth/Desktop/one.txt" or die "$!";
open  $h1, '<', $file1 or die "cannot open file1";
my @a1 = <$h1>;
close $h1;

#print grep {$_ !~ $match} @a1;
 print $f3 grep {$_ !~ $match} @a1;
[download]

referring to the previous scenario if my input file has texts along with numbers and special characters then how this partial mismatching is done.

 file1 contents:  1. Ram/is/going/reg[30]  2. he/is/coming/reg[31]  3.
+ what/goes/on/reg[32]
 file2 contents:  1. is/coming/reg[31]     2. on/reg[32]     3. try/to
+/do/reg[65]
 output file contents:  Ram/is/going/reg[30]
[download]

You appear to have forgotten to include your algorithm.

See also:

• How do I post a question effectively?
• Writeup Formatting Tips
• Short, Self-Contained, Correct Example
• I know what I mean. Why don't you?
• Is PM a good place to get answers for homework?

... special characters ...

I'm not sure what this thread is anymore (if it even really exists), but the handling of regex metacharacters or "special" characters is covered in haukex's Building Regex Alternations Dynamically article which I originally referenced here. Please read and understand it. And what hippo posted.

---

Give a man a fish:  <%-{-{-{-<

  use strict;
use warnings;

my $file1 = \<<"END1";
he/is/man/reg[30]
don't/you/reg[31]
what/goes/on/reg[32]
END1

my $file2 = \<<"END2";
/is/man/reg[30]
on/reg[32] 
try/to/do/reg[65]
END2

 
  
   open(my $f3, ">", "C:/Users/Siddharth/Desktop/do.txt")
    or die "Can't open < input.txt: $!";
open  my $h2, '<', $file2 or die "cannot open file2";
my @a2 = <$h2>;
close $h2;
chomp @a2;
my $match = join '|', @a2;
$match = qr/$match/;

open  my $h1, '<', $file1 or die "cannot open file1";
my @a1 = <$h1>;
close $h1;
 
my $fh = grep {$_ !~ $match} @a1;
print $f3 $fh;
#print grep {$_ !~ $match} @a1;
[download]