I am not sure what you are trying, but a few comments.

You declare my $empNUM; but later refer to $empNum - Possible Type ??

since you are using my try to be consistant.. so you line foreach $line (@line) would look like foreach my $line (@line)

instead of exiting I.e. exit 0; you might have employees to process after you found a match so instead do a next

So you might end up with something like

my $empNUM;

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

close(DATA);
close(UPDAT);
[download]

Update: Removed the foreach as it is not necessary..