My experience with this is using a photochemical-induced thrombosis model where the thrombus is formed in the mid- common carotid. I'm not sure what preparation you need for your electron microscopy, but I have previously tied off the vessel (with suture material) after occlusive thrombus formation and then removed the vessel by cutting it on either side of the thrombus. If your thrombus has developed in the mid common carotid there should be plenty of room to perform this.