To make the spectrum appear smoother, you can either apply a window function to the signal in the time domain by element-wise multiplication (MatLab offers window functions like blackman()/hamming()/hanning()/kaiser()/triang()/etc) before calulating the Fourier transform.
Or you apply a lowpass filter to the spectrum; however, in this case you need to make sure that no frequency shifts occur, for example by using filtfilt() instead of filter or by manually compensating any shifts the filter produces. The most practicable type of filter for this task is a symmetric FIR filter with even order.
