I thought i was going to have good clean power by coming directly off of a battery furthest from the alternator but once the engine starts i could see the alternator "noise" on every power lead. Turning on each accessory only made it worse which is why i was thinking of putting in a small isolation transformer or noise filter.
You can't use a normal isolation transformer in general because you need an AC waveform in order to switch the magnetic flux and couple power through. The DC needs to be converted to an AC signal, go through the isolation transformer and then converted back to a DC in order to work. Because of that, these packaged DC to DC isolated converters are more expensive.
You have to know how much current you plan to run through a DC to DC converter or isolators. They are not exactly cheap either for the DC-DC converters. This one below is only a 50W unit (12V at 4.17A) and its $150.
What you really need to do is find out what type of filtering you want. Most noise are high frequency noise from the alternator at 500 Hz or higher depending on the RPM. A low pass filter design that allows DC to go through but filters out high frequency noise seems like the better option from a cost point of view. Some of the simpler filters are just capacitors while others have toroidal inductors (sometimes called ferrite beads) in series to provide additional filtering. These inductors acts as RF chokes to suppress high frequency AC signals.
You can find these low pass filters relatively cheap on Ebay and many other places at around $15 for a 20A board. Personally, I haven't had the need to use one, so I haven't seen how well it filters. You may need to use a DSO (digital storage oscilloscope) to compare the waveform in the input to the output to see how well it cleans the signal. Most modern DSO has FFT (fast Fourier transform) to convert the signal to the frequency domain to be able to see the noise spurs at various frequencies. A spectrum analyzer or network analyzer would be better, but most of us can't afford that.
If you do plan to use an open design like this, you will need waterproof it with conformal coating and house it in some sort of plastic box to prevent moisture from getting in. I would also stake all the heavy parts like inductor and capacitors to prevent them from moving and causing the solder joints to fail in a high vibration environment. You can pot it with epoxy or use E6000/B7000 glue. Pot first, let it cure completely and then apply conformal coat. My conformal coat of choice is MG chemicals 422B or 422C silicon conformal coating. Stay away from Acrylic conformal coating. The material fluoresces under a UV light, so you can see how well you cover the parts. You may need to apply multiple coats to get all the nooks and crannies.
Good luck.
Dual filter:
Single filter:
