I am no expert and have no experience with these machines, but since no one else has responded, I will give you my thoughts. Assuming that the trees are growing in the area where the pond bowl and dam will go, then typically the top layer of topsoil must be removed down to good clay to excavate for the dam core. The stumps can be removed from the pond area and then returned if you want to use them for structure, or otherwise discarded or used for wildlife habitat. If you elect to grind them instead, then the chips will likely be mixed in with the topsoil when it is removed probably improving its consistency for growing plants later. If the topsoil is used behind and on top of the finished dam, this should not be a problem. Remaining roots in the pond area should be scraped out when excavating the top soil and any other layers of permeable soil. The important thing is to keep plant debris and permeable material out of the dam core and to have the pond bowl lined with impermeable material as well that is joined to the dam core. This typically means putting all permeable soil behind the dam. I hope this makes sense. Take pictures and post them!