boost converter
Just for clarity, I guess, you have a boost converter rather than a voltage inverter suggested by cokokerem?
As a first point, I expect that the circuit has a clear common ground, so it's basically meaningful to drain of capacitive coupled interference currents by an "Y" capacitor.
As a next point, the input and output ripple currents (a boost converter has mainly output ripple) should be filtered by series inductances and parallel capacitors ("L" or "Pi" filters).
Depending on the PCB design and acceptable interference level, some common mode interferences may persist. In this case, additional common mode chokes are an appropriate means, to my opinion.