One way to do this would be to use Photo Mechanic's "Copy/Move" utility. The first option in the Copy/Move dialogue decides what Photo Mechanic does when it encounters a RAW+JPEG pair. If its a JPEG on its own, it will copy/move it, if its a RAW on its own, it will copy/move that, but if its a RAW+JPEG pair, it will copy/move one or both based on your decision in that dropdown. If you copy everything into a subfolder, the new subfolder will contain all the files you want, and if you were moving files, rather than just copying, the original location will leave behind any of those JPEGs that were part of the pair.