You need to create a Hamming (or other method) window with a size in a power of 2 (I chose 1024 here). Then, apply the window to the Complex Signal before performing the Forward Fourier Transform.
string fileName = "mu1.wav";
WaveDecoder sourceDecoder = new WaveDecoder(fileName);
Signal sourceSignal = sourceDecoder.Decode();
//Create Hamming window so that signal will fit into power of 2:
RaisedCosineWindow window = RaisedCosineWindow.Hamming(1024);
// Splits the source signal by walking each 512 samples, then creating
// a 1024 sample window. Note that this will result in overlapped windows.
Signal[] windows = sourceSignal.Split(window, 512);
// You might need to import Accord.Math in order to call this:
ComplexSignal[] complex = windows.Apply(ComplexSignal.FromSignal);
// Forward to the Fourier domain
complex.ForwardFourierTransform(); //Complete!
//Recommend building a histogram to see the results