You haven't mentioned the frequency of the ripple. Is it AC mains? If it is, 0.1uF is too small a capacitor to smooth that ripple. I would say, a safe starting value should be in the 10s of uF. You also mention having a half wave rectifier prior to the measurement, so, you should be able to smooth it real good if you increase that capacitor.
Can you post a schematic? It might help understand the problem better.
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