#!/usr/bin/perl -w

use strict;

my @array = qw (biology_humananatomy_2 math_riemannhypothesis_1 biolog
+y_humananatomy_1 );
my @AoA;

for (@array) {
    push(@AoA,[split /\_/,$_,3]);
}

my @final = sort {$a->[0] cmp $b->[0] ||
                  $a->[1] cmp $b->[1] ||
                  $a->[2] <=> $b->[2]} @AoA;

for (@final) {
    print join('_',@$_),$/;
}
[download]

output:

biology_humananatomy_1
biology_humananatomy_2
math_riemannhypothesis_1
[download]

Please read other posts to understand why your code does not work.

cheers

SK