If this is not just for the sake of learning to use Perl, this type of task can be done with well known command line tools e.g. 
diff -n file1 file2 | egrep -v '^[ad]' > file3

[download]
will find the differences and write them to file3.

You may need to install cygwin or native versions of these tools.

In reply to Re: comparing 2 files and creating third file with uncommon content by Arunbear
in thread comparing 2 files and creating third file with uncommon content by rashichauhan

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