Manopidan,
I mistakenly assumed your question was about designing or modifying switched cap filters. When I posted my reply and backed out to the forum I then noticed your question appears in "Other Measurements". Let me revise my answer by posing a question:
Is your measurement intended for production automated test equipment (ATE) or for laboratory analysis?
For ATE I would suggest creating a "multi-tone" comprising frequencies below, near, and above the corner frequency. Choosing your test frequencies so they are related to your sampling frequency will give you very sharp frequency bin separation and eliminate the need for windowing. Ask your ATE vendor's FAE for details. (But now I wonder if capturing and checking a step response would provide adequate functional coverage, with shorter test time, for production testing? Related to my initial response.)
For laboratory analysis, I would suggest using a swept frequency source and a scope. Or you could do the same as in the ATE test using an arbitrary waveform generator and a spectrum analyzer.
Hope this is more helpful.
Bob P.
www.RPeruzzi.com