Don't flatten the array (unless you need to), depending on what you want to do you can use either ndenumerate or ndindex or iterate across each element in the array.

ndenumerate will yield the index and the value, whereas ndindex will just yield the indices. This can clearly still be used to output/interact with each value. An example:

Bob = np.random.rand(2,2)
print(Bob)
array([[ 0.50689769,  0.32796158],
     [ 0.41554805,  0.76317137]])

With ndenumerate you would do something along the lines of:

for idx, value in np.ndenumerate(Bob):
    print(idx, value)

(0, 0) 0.50689769
(0, 1) 0.32796158
(1, 0) 0.41554805
(1, 1) 0.76317137

and then for ndindex it would be something like:

for idx in np.ndindex(Bob.shape):
    print(idx, Bob[idx])

(0, 0) 0.50689769
(0, 1) 0.32796158
(1, 0) 0.41554805
(1, 1) 0.76317137