my $file = '/foo/file.txt';
open IN, $file or die "Can't read $file perl says $!\n";
my @lines = <IN>;
close IN;
for my $line (@lines) {
    # do stuff with the lines
}

# rewrite the file in its entirity
open OUT, '>$file' or die "Can't write $file perl says $!\n";
print OUT $line[0];        # print out the first line from the old file
print OUT @other_stuff;    # print whatever else you want
close OUT;