Selection of filters (common mode and differential mode)
But most of the said filters show impedance curves at frequencies
  greater than 1MHz. So, how can I select one for 100kHz ? Or is my
  thought process wrong ?


The flyback converter works with square waves when switching and it produces an array of harmonics that can still be significant past 1 GHz in some cases. This means that to prevent conducted emissions to the AC power (or DC feed to the power supply), a common mode choke may need to be "useful" above 1 GHz. 

Generally, in my experience (and broadly speaking) it's the 100 MHz range of frequencies that tend to be the normal problem area so, your common mode choke does need to be specified across a vast range of frequencies of which 100 kHz is the lowest.