There is more than one way to do trapunto. What method will you be using?
Typically what I would use for machine trapunto is medium or high loft polyester. Polyester tends to retain its loft better than cotton. This would be laid on top of whatever batting is used for the entire quilt. If the trapunto areas are quite small, say grape size, the medium loft might be easier to manage than high loft. Low loft typically will not give enough definition to make the extra work of trapunto worthwhile. However, there are some applications where it would be enough.
Much depends on how large the appliques are that you want to trapunto, and also how much quilting you want to do over the trapunto areas. If unsure, I would go with medium loft polyester.