A method of processing objects by a FIB (Focused Ion Beam) system and a carrier used therewith are provided. The carrier includes a carrying member and a processing portion having an object disposed thereon. Before the carrier is disposed into the FIB system, the carrying member is set to be flush in height with the processing portion having the object disposed thereon. After an eucentric height adjustment inside the FIB system, both the carrying member and the processing portion are in a same plane with the eucentric point of the system. Therefore, after the object on the processing portion is processed, a processed object or a processed block of the object can be moved to the carrying member without performing further eucentric height adjustment with respect to the carrying member.