Scenario: 

I am looking to make an alternator noise filter. I have A 120amp alternator that runs off a 5.5hp engine that I use out in the field. It keeps my battery around 13.8v and works well.

Consider the following:

Batteries normally absorb noise.  If a battery is across the alternator’s output, then the addition of a small bypass capacitor (say 1-10uf) may provide a path to earth for the remaining unwanted noise signals.

 

For filtering options on light loads, there are some over-the counter options, such as this one from Jaycar:

https://www.jaycar.com.au/10a-dc-noise-filter-improved/p/AA3074

 

If you want to make a higher current version, you would have to wind several turns of suitably heavy wire through some large ferrite rings, connected to the postive supply.  Then add a pair of large electrolytic capacitors either side of that choke to the negative terminal. This is called a Pi Filter.  (because this network resembles the symbol for Pi)

 

Another approach is to use a heavy transistor in series with the alternator output as an 'active filter'.

 

Have a look at this You Tube clip as it explains this principle quite well:

https://www.youtube.com/watch?v=wopmEyZKnYo

 

In each case we are trying to remove the noise by increasing the resistance path to high frequency noise while letting the clean DC component pass through unchanged.   

Capacitors connected across the positive and negative supply rail provide a short or 'bypass' for unwanted noise signals.