On the subject of how to properly remove a mesh, you would need to first dispose of its geometry and material, and then remove it from the scene.
const obj = scene.getObjectByName('meshy');
If your material has a texture, you need to dispose of that, too, using the dispose method of the Texture class. If you only remove the object from the scene, the memory allocated to your mesh won’t be freed up entirely, as the renderer still holds references to them (if I’ve understood things correctly).
Generally speaking, when it comes to cleaning up a scene, I would advise you to take a look at the docs and see which classes have a dispose method.