This is a reasonable expectation. Unfortunately in its current form, FFT does not support that exactly.
MatrixXcf B(3,10); // note the change from real to complex
//fft.fwd(B,A); // It is natural to want to do this, unfortunately it is not yet supported
// it works to iterate over the columns
for (int k=0;k<A.cols();++k)
B.col(k) = fft.fwd( A.col(k) );