the code is as follows , I hope now people can easily test it out and bring the best to me.

#!/usr/bin/perl -w

It's better to

use warnings;
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nowadays.

use Strict;
use File::Stat;
use Digest::MD5;

print "Enter the Path where all the data files are available:\t";
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Are you sure you want "\t" rather than "\n"?

$sourcedir= <STDIN>;
chomp($sourcedir);
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Since you're under strict this won't even compile. It is a good thing to post real code.

Update: Case matters! (Hadn't noticed your mistake in the first place.) Please (do a favour to yourself and) reread your program taking this into account.

open(LOG ,">>D:\\prad\\log1.csv");

It's better to

• use lexical FHs nowadays,
• use the three-args form of open(). (Opinions tend to vary on this, but as a general rule, I'd still recommend it.)
• use simple quotes (in this case) and use / as a directory separator even under Windows,
• always check open()s for success. A minimal

  open my $fh, '>>', 'path/to/file' or die $!;
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  can suffice.

I'm not reading the rest of your script. You should consider preparing a minimal, working, test program still exhibiting the problem you're concerned about and submit that. Chances are that in the process of doing so you will find the answer yourself...