This class wraps an internal Unity method that lets you to check if a ray intersects a mesh. Place it in an Editor folder.

RXLookingGlass.cs

using UnityEngine;
using UnityEditor;
using System.Collections;
using System;
using System.Linq;
using System.Reflection;

[InitializeOnLoad]
public class RXLookingGlass
{
	public static Type type_HandleUtility;
	protected static MethodInfo meth_IntersectRayMesh;
	
	static RXLookingGlass() 
	{
		var editorTypes = typeof(Editor).Assembly.GetTypes();
		
		type_HandleUtility = editorTypes.FirstOrDefault(t => t.Name == "HandleUtility");
		meth_IntersectRayMesh = type_HandleUtility.GetMethod("IntersectRayMesh",(BindingFlags.Static | BindingFlags.NonPublic));
	}
	
	public static bool IntersectRayMesh(Ray ray, MeshFilter meshFilter, out RaycastHit hit)
	{
		return IntersectRayMesh(ray,meshFilter.mesh,meshFilter.transform.localToWorldMatrix,out hit);
	}
	
	public static bool IntersectRayMesh(Ray ray, Mesh mesh, Matrix4x4 matrix, out RaycastHit hit)
	{
		var parameters = new object[]{ray,mesh,matrix,null};
		bool result = (bool)meth_IntersectRayMesh.Invoke(null,parameters);
		hit = (RaycastHit)parameters[3];
		return result;
	}
}