Creating smooth PWM response
You haven't given particulars, but it looks like you are seeing the result of individual PWM pulses.  If so, and that's not what you want, then you need to low pass filter the PWM output more.

The low pass filter should be attenuating the PWM frequency to below your maximum noise limit.  It is apparently not doing this, so needs to be re-designed.

As high as possible PWM frequency helps.  That leaves more frequency ratio between the PWM frequency and the highest frequency of interest.  That in turn makes it easier to attenuate the PWM frequency while not attenuating the desired frequency.