For a very shy turtle, the best way is for an experienced person to trim the nails. A herp vet would be your best bet, and you may have to leave the turtle in the care of the facility due to the shyness of the turtle. I would ask the vet that he/she do it and not one of his staff, because they may not be very good at it.

If you do it yourself-read my online book to see how to do it. It takes only a steady, firm hand. You grab the foot and carefully cut the nails, avoiding the quick-using a large clipper, or a small dog's nail clipper. Beaks should be trimmed with a dremel tool, not clippers, or shears.
Tess