In order to get prey from the town hall or clan fortress, you need to completely destroy them.

The clan’s town hall and fortress are not capable of resisting spells, which means that earthquake and lightning spells can seriously harm them.

Also remember: there is no guarantee that there is any prey there. Only part of the production is stored in the town hall (not that which was not collected from mines, wells and collectors). And only military and star bonuses are stored in the fortress.