This function requires two 1xN array of points, how does that work? Maybe 1xNx2 would be more clear. You need to convert the point array to the shape (1,N,2). If your point array looks like mine:

a3xN = \
array([[35, 59, 32, 92, 71, 12,  4,  8, 28, 19],
       [ 9,  4, 36, 80, 85, 47, 60, 83, 38, 68],
       [ 1,  1,  1,  1,  1,  1,  1,  1,  1,  1]])

You need to change it to look like this:

a1xNx2 = \
array([[[35,  9],
        [59,  4],
        [32, 36],
        [92, 80],
        [71, 85],
        [12, 47],
        [ 4, 60],
        [ 8, 83],
        [28, 38],
        [19, 68]]])

Try this:

a1xNx2 = r_[[a3xN[:2].T]]
#or
a1xNx2 = array([a3xN[:2].T])

The output is in the same form. Use output[0].T to convert to a 2xN array. If you don’t need the original a3xN array, then copy the output 2xN into the first two rows of a3xN (a3xN[:2] = output[0].T). Or convert to homogeneous coordinates like this:

outa3xN = append(outa[0].T,ones((1,len(outa[0]))),0)
#or
outa3xN = vstack((outa[0].T,ones(len(outa[0]))))

Complete example:

# A fundamental or essential matrix
F3x3 = array([[ 0.0345, -0.2073, -0.0673],
              [-0.1403, -0.0003,  0.6889],
              [ 0.0604, -0.6725,  0.0349]])
# Homogeneous 2D point arrays
a3xN = array([[35, 59, 32, 92, 71, 12,  4,  8],
              [ 9,  4, 36, 80, 85, 47, 60, 83],
              [ 1,  1,  1,  1,  1,  1,  1,  1]], float)
# Pass an integer array and get an integer array back
b3xN = array([[95, 24, 86, 26,  4, 85, 68, 66],
              [35, 44, 91, 10, 14, 41, 93, 34],
              [ 1,  1,  1,  1,  1,  1,  1,  1]], int)
# The cv2 method
outa, outb = cv2.correctMatches( F3x3, r_[[a3xN[:2].T]], r_[[b3xN[:2].T]] )
# Two ways of making the output homogeneous
outa3xN = append(outa[0].T,ones((1,len(outa[0]))),0)
outb3xN = vstack((outb[0].T,ones(len(outb[0]),int)))
print outa3xN
print outb3xN

[[ 34.37  52.71  12.63  94.56  70.1    5.   -24.92 -14.35]
 [ -1.31 -15.19  -3.31  77.    85.69   0.48  35.01  77.4 ]
 [  1.     1.     1.     1.     1.     1.     1.     1.  ]]
[[ 96  36  88   6  -8  85  49   4]
 [ 33  28  89 -10   7  41 103  44]
 [  1   1   1   1   1   1   1   1]]

Note that if you pass an integer array, then the function returns an int array, so you may need to convert to float first.