This work investigates three-phase electromagnetic interference(EMI) conducted emission(CE) measurements with the aim to separate the noise voltages in their common-mode(CM) and differential-mode(DM) parts. By doing so, the converter input and/or output filter stages can be individually optimized to improve the CM or DM attenuation depending on the origin of the CE disturbances. An overview of various ways to achieve this separation is provided and an active three-phase noise separator is presented. The main advantage of the presented active solution is the absence of magnetic components in the signal path which drastically facilitates the matching at high frequencies. The influence of asymmetries and mismatches of the component parasitics as well as in the circuit board layout are analyzed. To assess the performance of the proposed system according to widely known metrics such as CM and DM transfer functions and rejection ratios, different test methods are established and the implied limitations regarding maximum measurable performance are considered. Finally, experimental results verifying the calculated separation capabilities are provided.