User blog comment:Assembled1801/Supergirl (CW) vs Raiden (Metal Gear)/@comment-5078776-20171021013724/@comment-5078776-20171023011300

"This oscillation weakened the molecular bonds of anything it cuts..."

- Metal Gear wiki

"Weakens" doesn't necessarily mean it will cut through them outright. That's the reason why Raiden's blade doesn't work on Armstrong in the beginning- he had to weaken Armstrong's NANOMACHINES SON to the point where the HF Blade could do it's job.

Plus, there is a difference between Barry's phasing and this- while the HF Blade weakens molecules, Barry simply moves his body at a fast enough speed to phase through solid, more dense objects. He doesn't do anything to the opposing object's atoms- he simply changes his own.