A method of measuring an overlay of an object is provided. In the method, first information of a first structure may be obtained. A preliminary structure may be formed on the first structure. Second information of the preliminary structure may be obtained. The first information and the second information may be processed to obtain virtual information of a second structure that would be formed on the first structure if a process is performed on the preliminary structure. A virtual overlay between the first structure and the second structure may be measured using the virtual information.