use File::Slurp;
my @file1 = read_file('file1');
my @file2 = read_file('file2');

##</code><code>##

my $lines = merge_lines(\@file1, \@file2);
write_file('file3', @$lines);

##</code><code>##

sub merge_lines {
    my ($lines1, $lines2) = @_;
    my @lines;
    ....
    return \@lines;
}