Two key questions....what kind of trees and what kind of thistles...
Third question...do you have a Restricted Use Permit?


If deciduous trees, you can apply a fall application of a couple different products that will control biennial thistles (Musk or Bull)

If they are Canada Thistles, you have a chore in front of you but its not all that bad. There are a couple excellent products for Canada thistles, again that can be used around deciduous trees.

Give me some more info and perhaps I can help...