I have managed browse each point and convert the coordinate, and get the voxel value at this local coordinate,
Great so you have replaced vtkProbeFilter (if you correctly added the voxel value into a vtkDataArray( e.g. vtkDataArray.newInstance({name: 'scalars', values: new UInt16Array(scalarValuesHere), numberOfComponents: 1});
The next step is directly apply a transformation filter to my vtkPolyData?
You can use vtkMatrixBuilder.buildFromDegree().scale(...).apply(polyData.getPoints().getData()) to apply a transform on ALL the vtkPolyData points.