How to extract the switching noise component for this signal data?
If I'm interpreting your first scope plot correctly it's showing switching noise from a SMPS running just under 100KHz.  The apparent jitter is due to the fact that noise occurs on both edges of the switching waveform, so analysis of this waveform will show a fundamental at just under 200KHz, spread somewhat by the jitter on the switching edge.  You can see this nearly buried in the noise on your first frequency plot.

However, there's very little fundamental in this waveform.  Most of the energy is in the ringing, which you can see in the higher order spectral content.