I'd use a global regex to extract just the digits directly into an array:

use warnings;
use strict;

my $string = 'MD:Z:4C3C7C0T2^T9C44';

my @nums = $string =~ /\d+/g;

print "$_\n" for @nums;
[download]

Output:

4
3
7
0
2
9
44
[download]