Say that you read each file into an array.

use File::Slurp;
my @file1 = read_file('file1');
my @file2 = read_file('file2');
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Where would you go from there? Eventually you could have a new array, write it out like this:

my $lines = merge_lines(\@file1, \@file2);
write_file('file3', @$lines);
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How would you write 'merge_lines'?

sub merge_lines {
    my ($lines1, $lines2) = @_;
    my @lines;
    ....
    return \@lines;
}
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Not the most efficient way to do it, but...