The Molecular Separator Ray is a moderately small object that is red in color. It also has holes in the front where the rays are shot from. It is similar to the flamethrower Patrick used in "No Nose Knows."
When Sandy's transporter fails, resulting in SpongeBob and Squidward morphed together, Sandy has to build a new invention to reverse the effects. Squidward demands and begs Sandy to build it before the night of his clarinet recital. The following night, Sandy does not appear with the machine, and Squidward has to play his clarinet even if he is still morphed with SpongeBob (albeit wearing a cloak to mask SpongeBob). In the middle of the recital, the cloak falls off, revealing themselves as one body of two persons. Eventually, Sandy comes in with the Molecular Separator Ray and changes the two back into individual bodies. Squidward's audience leaves, causing Squidward to overload the systems by pushing many buttons at a time to bring them back. This results in a reversed function which morphs many characters into Squidward.