Khelz
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Are you sure it's the HV supply and not pickup from the mains radiation? Certainly you can add additional filtering for the HV supply output, it that helps. If the load current is small you could use a simple RC filter but the capacitor would need a voltage rating over 3.5kV.
What is the value of the shunt resistor R1? Are the leads twisted-shielded from R1 to the amp input.
Another approach often used is a notch filter at the 60Hz line frequency. Those can provide significant rejection without significantly affecting signals on either side of that frequency.
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