Coordinate measuring machines (CMMs) are very versatile devices, and they are widely used in industry because they can measure all types of three-dimensional shapes. In recent years, coordinate measuring machines have become indispensable for quality control management. With industrial globalization, it is necessary to estimate uncertainty in measured values to ensure measurement traceability. However, it is difficult to ascertain the uncertainty of a coordinate measuring machine because there are many factors causing uncertainty, such as the size of the device itself and the complexity of the structure. In this study, we focused on a method of estimating uncertainty through computer simulation, as proposed in ISO 15530:2008. We estimated uncertainty by using Virtual CMM, a Monte Carlo simulation method proposed and developed by Physikalisch-Technisch BUndesanstalt in Germany. Virtual CMM has been introduced by Mitutoyo, Carl ZEISS, and Hexagon Metrology. Among these software, we used Virtual CMM by Mitutoyo and Carl ZEISS. The hole plate used in this study have values calibrated by NMIJ (National Metrology Institute of Japan) and was also used to calibrate the coordinate measuring machine. The results of consistency evaluation from the En number confirmed that the calibration values were consistent with each other.