First, create C:
C = zeros(size(B));
Then use this command to assign elements of B associated with nonzero A values into the corresponding locations in C:
C(A~=0) = B(A~=0);
If the values in A are not exactly zero but really tiny, then create a threshold
thresh = 1e-6; % 10^(-6) for example
And use this threshold as follows
C(abs(A)>thresh) = B(abs(A)>thresh);
