1. Field of the Invention The invention is generally related to the area of semiconductor manufacturing and more particularly to a method of compensating for misalignment caused by critical dimension variation in chemical mechanical polishing process. 2. Description of the Related Art Chemical mechanical polishing (CMP) is a planarizing process used to polish down and/or remove wafer features. The surface of wafer on which wafers have been processed by CMP process, is not flat, which causes CMP tool alignment problem. CMP tool misalignment problem is caused by the wafer-to-wafer variation of wafer thickness. Since CMP polishing rate is a function of the wafer thickness variation and CMP tool alignment accuracy, the CMP tool misalignment problem would cause poor wafer surface condition. U.S. Pat. No. 6,664,966, granted to Liang, et al., discloses a two-step polishing process. The first step removes the major portion of material from the center of the wafer and the second step removes the rest of the material from the perimeter. The two-step CMP process has less variation in wafer surface to be processed by the CMP process. U.S. Pat. No. 6,531,231, granted to Chen, et al., discloses a method of using a dummy pattern with special profile to compensate for the thickness variation of the wafer in order to minimize wafer-to-wafer thickness variation during CMP process. U.S. Pat. No. 6,972,280, granted to Huijbregts, et al., discloses a method of using a dummy ring to compensate for the thickness variation of the wafer during CMP process. The dummy ring is used to replace the dummy pattern in the prior art. In order to maintain the uniformity in polishing, dummy ring provides a flat surface during the polishing process. U.S. Pat. No. 6,917,638, granted to Liu, et al., discloses a method of using a dummy pattern with special profile to compensate for the thickness variation of the wafer during CMP process. In addition to the dummy pattern, dummy wafer ring is used to compensate for the thickness variation of the wafer. The dummy pattern and dummy wafer ring are used to improve the wafer flatness after the CMP process. Therefore, a need exists in the industry for a method of improving wafer surface condition without reducing the throughput and uniformity.