I think intersectsMesh() is faster, because you can prepare meshes, that gets evaluated with your ray intersection, in an array. While on pickWithRay you have to always go through all meshes of the scene and i.e. use a condition (predicate) to determine if a mesh of the scene is part of this type of your custom intersection evaluation. Another option is mesh.intersects(), which seems to have even more options to increase performance. Source: SolidParticle.intersectsMesh() or Scene.pickWithRay() or Ray.intersectsMesh()
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