open the file for simple output (not for append, just plain old simple output). If the file open is successful, the file will be truncated, as per the POD: open.

{    
    open my $wipe_file, '>', $filename or die $!;
    close $wipe_file or die $!;
    #done
}
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It would be wise to lock the file beforehand so that you know nobody else is using it at the moment. ...doesn't seem prudent to obliterate the contents of a file that's currently being read by some other process, now does it?

At any rate, opening a file for output, by default, truncates the file to zero length.