We can't help much with only screenshots to look at. You can design many different filters depending on the exact structure of your noise.
For stationary noise, you should start by doing spectral analysis on your signal to identify the noise characteristics. Try for example to calculate and display the power spectrum of your signal.
If the noise is significantly higher (in frequency) than your bandwidth of interest you can try to apply a lowpass filter to your signal.
If it is limited to a narrow frequency range, maybe a bandstop filter is better
Pulsing noise, like it look you also are having issues with, may be more challenging to characterize. Try to take a subset that almost only include your pulsing noise and check it out with a power spectrum.
Your last screenshot shows a noise level in the order of 4-5 lsb RMS of your measurement device. That signal is pretty smaal. However if it is a problem, you may want to play with signal scaling, so amplify your signal before quantizing it with your acquisition board and correct the gain boost correspondingly in software.
Important note: Since you are dealing with a servo system, be aware that any filtering may/will affect the stability of your control loop, so you may have to be careful with too much filtering and also have to re-adjust your loop parameters.
