Hi, when i did my M. D. i worked with M. fijiensis, an mielin-rich fungus wihch is really dificult to be cleaned so, for RNA extraction we used lactophenol extraction method and we got excelen results. You can use the QIAquick cleaning kits to improve your extractions, just be sure to use a good quantity of raw material.
Lactophenol destroys the parasite DNA and should not be used for any specimens that you are planning to take DNA from later. For most nematodes, you can take part of mid-body for molecular work, and use the anterior and posterior end for morphological study.