How to properly mask a numpy 2D array?

Is this what you are looking for?

import numpy as np
x[~np.array(mask)]
# array([[1, 2],
#        [2, 3]])

Or from numpy masked array:

newX = np.ma.array(x, mask = np.column_stack((mask, mask)))
newX

# masked_array(data =
#  [[1 2]
#  [2 3]
#  [-- --]],
#              mask =
#  [[False False]
#  [False False]
#  [ True  True]],
#        fill_value = 999999)