This paper presents an optimization method to filter out the noise from an isolated DC-DC converter in order to prevent the effect on small-signal measuring circuits. In general, there are many high voltage applications that require galvanic isolation for a power supply to provide power to different electrical components, thereby protecting sensitive circuits from high voltage spikes, safety and floating ground requirements. But all isolated DC-DC converters have switching devices that generate noise. The noise is mainly common mode noise. It will be transmitted from input (primary) to output (secondary) by coupling capacitance within the converter, then the output waveform captured will be overlapped with ripple (probably hundreds of KHz switching frequency) and high-frequency noise (up to 20MHz) which will affect the measuring accuracy. The proposed method here is intended to provide a reference in your future designs and eliminate the effects from an isolated DC-DC converter.