In scientific writing, it is correct to write something like
The filter-based method is good.
But what if I have two nouns before
-based? Something like
The lowpass filter-based method is good.
Is it still correct?
If lowpass modifies method --if it's the lowpass method --then leave it as it is. If lowpass modifies filter, then all three words should be hyphenated together, as in "The lowpass-filter-based method is good." You could also probably get away with "The lowpass-filter based method is good."
Basically the rule is you want to reduce the ambiguity by showing which words modify which other words. You can theoretically have a whole bunch of hyphens in a row, although you'd want to avoid that if you can, since there's no further way to indicate within the string which words modify which others.
I've also read that it is acceptable to put an en (long) hyphen between the compound noun and the adjective ("lowpass filter–method"), so that the compound noun itself does not need to be hyphenated.