# Open a different file as a semaphore lock
open my $SEM, ">the_file.semaphore";
flock($SEM, LOCK_EX);       # lock it

# then process the Real File
open my $FH, "the_file";
my @lines = <$FH>;         # read it
# because we never fiddle with $SEM, we still have a lock
open $FH, ">the_file";     # open for writing.
push @lines, "new line\n"; # process the lines
print $FH for (@lines);    # write them out
close $FH;                 # close the file

close $SEM;                # close and unlock semaphore