The first step needs to be to find the indices of the array that correspond to the conditional statement. You can use something like find for this, but logical indexing is usually preferred.
y = ones(size(A));
ind = A >= C;
y(ind) = 0;
y(~ind) = 1;
The last line is not absolutely necessary in this case, since we initialized y using ones, but you could put an equation here if something more complicated was needed.