Thanks for yout inputs. The below code is how I got the output I wanted.

#!perl
open FILE1, "<file1"; @linesFile1 = <FILE1>; close FILE1;
open FILE2, "<file2"; @linesFile2 = <FILE2>; close FILE2;
open(MYOUTFILE, ">file3");
open(MYOUTFILE, ">>file3");
foreach $line(@linesFile1)
{
    if(! grep{$_ eq $line} @linesFile2 ){ print MYOUTFILE "$line"; }
}
print "\n";
close(MYOUTFILE);
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Thanks again.. RCP