Three-dimensional (3D) geological model, as an effective tool for modelling the complex nature of underground geological conditions, has been used for the design and construction of underground facilities. The accuracy and reliability of the geological information reflected by the 3D model are critical for engineering practitioners to make sound judgement. It is important to consistently update the 3D geological model with new borehole or geophysical data for better assessment of the underground uncertainties. In this study, an application of the NTU-BCA 3D geological model to an undergoing subway project in Singapore has been investigated. The established 3D geological model was updated using the new borehole data obtained in the project. A comparison of the virtual boreholes generated in the 3D model with the real borehole data in terms of rockhead positions was made as a verification of the uncertainties of the model. The uncertainties analyses show that the standard deviations of the predicted errors for the rockhead are improved after the new borehole data was incorporated into the model. Predictions made by spatial statistical analyses are also presented and compared with the borehole data and the results from the 3D geological modeling. Through the study, an example for using newly obtained borehole data to update the existed 3D geological model to improve the accuracy was given.