How to delete certain element(s) from an array?

you can use pop on the list item. For example -

>>> array = [[1,2,3,4], [6,7,8,9]]
>>> array [1].pop(3)
>>> array 
[[1, 2, 3, 4], [6, 7, 8]]

I think this can solve your problem.

x = [[2,3,4,5,2],[5,3,6,7,9,2],[34,5,7],[2,46,7,4,36]]
for i in range(len(x)):
    for j in range(len(x[i])):
        if j<len(x[i]):
            if x[i][j] == 2:
                del x[i][j]

I have tested it locally and working as expected.Hope it will help.

Mutating a list while iterating over it is always a bad idea. Just make a new list and add everything except those items you want to exclude. Such as:

x = [[2,3,4,5,2],[5,3,6,7,9,2],[34,5,7],[2,46,7,4,36]]
new_array = []
temp = []
delete_val = 2

for list_ in x:
    for element in list_:
        if element != delete_val:
            temp.append(element)
    new_array.append(temp)
    temp = []

x = new_array
print(x)

Edit: made it a little more pythonic by omitting list indices.

I think this is more readable at the cost of temporarily more memory usage (making a new list) compared to the solution that Sai prateek has offered.