IMO OP does not actually want np.bitwise_and() (aka &) but actually wants np.logical_and() because they are comparing logical values such as True and False - see this SO post on logical vs. bitwise to see the difference.

>>> x = array([5, 2, 3, 1, 4, 5])
>>> y = array(['f','o','o','b','a','r'])
>>> output = y[np.logical_and(x > 1, x < 5)] # desired output is ['o','o','a']
>>> output
array(['o', 'o', 'a'],
      dtype='|S1')

And equivalent way to do this is with np.all() by setting the axis argument appropriately.

>>> output = y[np.all([x > 1, x < 5], axis=0)] # desired output is ['o','o','a']
>>> output
array(['o', 'o', 'a'],
      dtype='|S1')

by the numbers:

>>> %timeit (a < b) & (b < c)
The slowest run took 32.97 times longer than the fastest. This could mean that an intermediate result is being cached.
100000 loops, best of 3: 1.15 µs per loop

>>> %timeit np.logical_and(a < b, b < c)
The slowest run took 32.59 times longer than the fastest. This could mean that an intermediate result is being cached.
1000000 loops, best of 3: 1.17 µs per loop

>>> %timeit np.all([a < b, b < c], 0)
The slowest run took 67.47 times longer than the fastest. This could mean that an intermediate result is being cached.
100000 loops, best of 3: 5.06 µs per loop

so using np.all() is slower, but & and logical_and are about the same.

Fancy indexing requires you to provide all indices for each dimension. You are providing 3 indices for the first one, and only 2 for the second one, hence the error. You want to do something like this:

>>> a[[[0, 0], [1, 1], [3, 3]], [[0,2], [0,2], [0, 2]]]
array([[ 0,  2],
       [ 4,  6],
       [12, 14]])

That is of course a pain to write, so you can let broadcasting help you:

>>> a[[[0], [1], [3]], [0, 2]]
array([[ 0,  2],
       [ 4,  6],
       [12, 14]])

This is much simpler to do if you index with arrays, not lists:

>>> row_idx = np.array([0, 1, 3])
>>> col_idx = np.array([0, 2])
>>> a[row_idx[:, None], col_idx]
array([[ 0,  2],
       [ 4,  6],
       [12, 14]])