A spectrum analyzer for measuring an RF signal over a selected frequency span configured to use multiple Intermediate Frequencies (IFs) for residual, spurious and image signal reduction. The spectrum analyzer has both a primary IF path and a secondary IF path configured to provide band pass filtering of the IF signals. A master clock synthesizer is configured to reduce residual noise by providing from a single Voltage Controlled Oscillator, a master clock signal and a Local Oscillator (LO) signal. The spectrum analyzer has a microcontroller configured to change the frequency of the master clock signal and the LO signal if the center frequency of the selected span is sufficiently close to a known spurious signal.