Storing scalar numerics in cell arrays will make your processing pointlessly complex, so I will presume that you actually sensibly store your numeric data in simpler and more efficient numeric arrays. Then your task is easy:
>> Swapping = [1,1,1;1,5,1;2,3,4]
Swapping =
1 1 1
1 5 1
2 3 4
>> C1 = [59,57,46;4,39,35;8,22,20]
C1 =
59 57 46
4 39 35
8 22 20
>> result = C1 .* (Swapping==1)
result =
59 57 46
4 0 35
0 0 0
