... operate with only file locations ... not ... texts of file in program ...

Opening files for reading in the "normal" way (as opposed to the ramdisk-ish approach used for convenience in the example code) is straightforward and is well described in the open and perlopentut docs. Maybe also take a look at Files and I/O in perlintro.

... print the output in other file.

This merely involves opening a write filehandle (see docs referred to above) inside the Perl script and print-ing to this filehandle rather than to STDOUT by default, or else redirecting standard output from the Perl script as a whole to a file via the OS command line (see your OS docs regarding I/O redirection).

Update: Minor wording changes to (hopefully) enhance clarity.

• problem description
  here, the monks already gave you some hints, especially towards the end of Re^3: partial matching of lines in perl
• implementation
  here, I'd like to refer you to perlintro. regarding your last question, see the section on files and I/O

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;
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2020-06-21 Athanasius added code tags.

please tell me the problem occuring in this program,because it is giving nothing in the output file.Input file contents are same as told earlier.

You have

use warnings;
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at the top of your program.

When you run your program, Perl will tell you at least one problem in your program immediately:

perl -wle 'open my $fh, "<", "test.txt"; print $fh "hello"'
Filehandle $fh opened only for input at -e line 1.
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If you don't get this output, please either post the real code you are using or find a way to see the output of your program.