my $empNUM;

open(DATA, "data") or die ; 
open(UPDAT, ">updated") or die;
while(<DATA>)
{
    my @line = split(/\s+/, $_); #Assuming your file is split on multiple spaces..?
    if ($line[2] eq $empNUM){ 
        next;
    }
    else {
        print UPDAT "$_";
    }
}

close(DATA);
close(UPDAT);