• You don't need to use system "rm file2" as open(FILE2, ">file2") will delete the file if it exists.
• You should always verify that the files were opened correctly before trying to use a possibly invalid filehandle.

You probably want something like this:

open FILE2,       '>', 'file2' or die "Cannot open 'file2' $!";
open MYINPUTFILE, '<', 'file'  or die "Cannot open 'file' $!";
                  
while ( my $line = <MYINPUTFILE> ) {
    chomp $line;
    print FILE2
        "$line\n",
        "you need to do this\n";
}

unless ( $. ) {
    print FILE2 "There is nothing to do\n";
}
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