I really do not understand your requirements. My best guess is you want to partition the array @arr1 according to the specification in the first column of array @a1. (and @arr2 according to the second column.) The 'end' indicies in @arr2 follow the math convention of 'start-at-one' rather than Perl's 'start-at-zero'. You are having a problem with the partitioning, not writing to files. The following code only does @arr1 and does not produce exactly what you expect. I hope you can use it as an example when you repost your question.

use strict;
use warnings;
my @arr1 = 'a' .. 'j';

my @al = (
    # Arr1  Arr2
    [  3,     4  ], 
    [  5,     5  ], 
    [  6,     6  ], 
    [  8,    10  ], 
);
my $start = 0;
my $end = 0;

for my $i (0 .. $#al) {
    $end = $al[$i][0]-1;
    print @arr1[$start .. $end], "\n";
    $start = $end+1;
}
[download]

OUTPUT:

abc
de
f
gh
[download]