Untested code, but something along the lines of this should work (I'm assuming @MDarray is already defined):

my @number = qw(2 3 4 5);
my $curr_array = \@MDarray;

while ($#number > 0) {   # Stop when 1 element left
  my $index = shift @number;
  $curr_array = @$curr_array[$index];
}
@$curr_array[$number[0]] = # Do something
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Since multi-dimensional arrays in Perl are just arrays of arrayrefs (of arrayrefs of...), this starts with a reference to the top-level array, then walks down through each level, getting the reference to the next level, until it reaches the end.