noise filter

I have a question about using rca style noise filters. I have alternator whine at low engine idle. I have removed the head unit and ran a seperate power and grd wire and a noise filter on both grd, power side of head unit. but the problem is still there. If I unplug the output rca connector from the head unit to the first amp I have and run the engine noise will go away. I installed a scosche es-034 grd isolator in the rca hook up and noise goes away but I was worried about this affecting my signal output "SOUND QUALITY" I was trying to fix the problem without messing with any of the signal wires. Any ideas would be appreciated.--zx9r

Yes, replace RCAs and also check for good ground on your amp.  It is also possible you have a speaker wire (or a stray strand from a speaker wire) that is touching a ground between the amp and the speakers, but not too likely if the Scoche ground isolator helps.