You got a lot of readin' to do there fella ;-) Simply open() the file and print() to it

use strict;

my @atoms = qw(123 456 789);

# use: open(FH, ">somefile.txt") if perl -v < 5.6.0
open(my $fh, ">", "somefile.txt") or die("ack - $!");
print $fh $_,$/ for @atoms;
close $fh;

__END__

shell> cat somefile.txt
123
456
789
[download]

If you're talking about a multi-dimensional array then it would be something like this

my @atoms = ([qw(123 231 312)], [qw(456 564 646)], [qw(789 897 978)]);
open(my $fh, ">", "somefile.txt") or die("ack - $!");
print $fh "@$_", $/ for @atoms;
close $fh;

__END__

shell> cat somefile.txt
123 231 312
456 564 646
789 897 978
[download]

For more info on opening files in perl see the perlopentut man page, and check out perldata and perlref for info on the likes of multi-dimensional arrays in perl.
HTH

_________
broquaint

update: added how to print out mutli-dimensional arrays (thanks to gmax for the tip)