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Ralf, using FFT for noise reduction is quite unusual. I don't believe that much success can be achieved this way. My guess that issue you having with Filter block is that it does not configures well for very low frequencies (<50Hz), so you still have a lot of AC noise. It is possible to cheat the Filter and get into ~1 Hz low-frequency cut-off. Try to set Filter to low-pass with cut-off 100 Hz, and input frequency 1 kHz, but feed Filter input with 10 Hz (using DMA or direct write), you should get effective filter cut-off at about 1 Hz. Using FIR setting, I was able to get about 1-2 Hz cut-off, but not 0.1 Hz.
Other thing is that for low frequency measurements the Filter is overkill, you can make simple IIR filter in code with very long decrement time. See also KBA
Other issue can be type of noise from cap sense. Inspect the output for possible spikes (non-random noise). This kind of noise will not be removed by the Filter. I would try to use a median filter before the Filter block (see link below)
Hello anks & odissey1,
thank you for your hints. I'll try that and compare the results.