Could you please tell me anyways or give me some examples of including an EMI filter (which has common mode, and differential mode chokes and x cap, y caps)in PLECS.
One can construct a model of the passive components of your EMI filter using basic components from the PLECS library. For example, the “Mutual Inductor” component is appropriate for common mode chokes with mutual coupling.
However, note that if you employ the standard ideal switch model in PLECS there will be a natural limitation regarding the accuracy of the calculated spectrum because the switching transition itself is not modeled. If you are interested in the spectral components that are natural harmonics of the switching switching frequency (multiples) then PLECS may provide sufficient detail.
If you want to analyze higher frequencies where the switching transitions and other parasitics are critical, you may want to consider a different type of simulation or directly a hardware measurement.