Dan, Did you try editng the point cloud (https://support.pix4d.com/hc/en-us/articles/202560499-How-to-edit-the-point-cloud-in-the-rayCloud)? You can classify the point cloud, put the trees in the disabled group, save the project and then process step 3. Also, have a look at this community post: Remove vegetation from orthomosaic - #6 by Ivan_Radan, might be helpful.