The best EMI filter is the one that you don't need. So you'd typically start by running the circuit in SPICE, and add parasitic properties of key elements. E.g. decoupling capacitors have ESR and ESL (equivalent series resistance and inductance, respectively). That way, the AC current flowing from the power source is more realistic. And so you know exactly what frequencies are there. Next, your goal is to make those AC currents flow inside your circuit and not reach the power supply. The first step will be to arrange circuit impedances such that most of the AC current flows in small loops. Some of it will inevitably escape due to nonidealities of components and layout, and that's the part that the EMI filter would deal with.

The approximate process would be as below, and some groups of steps have to be iteratively repeated.

1. Design the basic circuit and get it to work in SPICE at least.

2. Choose actual components (real part numbers).

3. Use the component data sheets and/or characterize the components using a network analyzer to obtain their accurate simulation models that include parasitics.

4. Substitute equivalent networks of real, non-ideal components for the ideal components in the SPICE model.

5. Identify the AC current loops of concern in the SPICE model.

6. Lay out the circuit taking critical current loops into account.

7. Use an electromagnetic simulator - this could be your head, with enough experience - to approximate the parasitics of the layout.

8. Add the layout parasitics to the SPICE model.

9. Re-run the simulation and observe the AC currents flowing from the power source.

10. Do various things to constrain those currents to flow within your circuit only. The EMI filter is the last line of defense that will do that.