I have my doubts as to whether it would be cost effective enough to filter out everything but the long chain hydrocarbon molecules (in the case of biodiesel), t

I have my doubts as to whether it would be cost effective enough to filter out everything but the long chain hydrocarbon molecules (in the case of biodiesel), though ethanol based fuels might be better as they already have to be fairly well purified. Really depends on the individual chemistry I guess. Hopefully the waste isn't too contaminated.