Example Node.js script using glTF-Transform to extract geometry from a glTF document and create a geometry-only three.js scene graph.

EXTRACT_GEOMETRY.mjs

import { NodeIO } from '@gltf-transform/core';
import { KHRONOS_EXTENSIONS } from '@gltf-transform/extensions';
import draco3d from 'draco3dgltf';

// set up I/O
const io = new NodeIO()
  .registerExtensions(KHRONOS_EXTENSIONS)
  .registerDependencies({'draco3d.decoder': await draco3d.createDecoderModule()});

const document = await io.read('path/to/file.glb');
const scene = document.getRoot().listScenes()[0];

const group = new THREE.Group();

// traverse the scene, adding only nodes with geometry
scene.traverse((node) => {
  if (node.getMesh()) {
    group.add(createGroup(node));
  }
});

/** 
 * Creates THREE.Group for a glTF-Transform Node. Considers only vertex positions,
 * other vertex attributes and materials are ignored. For a 'full' implementation,
 * see https://github.com/donmccurdy/glTF-Transform-View.
 */
function createGroup(node) {
  const group = new THREE.Object3D();
  const matrix = new THREE.Matrix4()
    .fromArray(node.getWorldMatrix());
  matrix.decompose(
    group.position, 
    group.quaternion, 
    group.scale
  );

  for (const prim of node.getMesh().listPrimitives()) {
    const position = prim.getAttribute('POSITION');
    const indices = prim.getIndices();

    const geometry = new THREE.BufferGeometry();

    geometry.setAttribute(
      'position', 
      new THREE.BufferAttribute(
        position.getArray(),
        position.getElementSize(),
        position.getNormalized()
      )
    );

    if (indices) {
      geometry.setIndex(new THREE.BufferAttribute(indices.getArray(), 1));
    }

    group.add(new THREE.Mesh(geometry));
  }
  
  return group;
}