We present a calibration method of a time-of-flight (ToF) sensor and a color camera pair to align the 3D measurements with the color image correctly. We have designed a 2.5D pattern board with irregularly placed holes to be accurately detected from low resolution depth images of a ToF camera as well as from high resolution color images. In order to improve the accuracy of the 3D measurements of a ToF camera, we propose to perform ray correction and range bias correction. We reset the transformation of the ToF sensor which transforms the radial distance into the scene depth in Cartesian coordinate through ray correction. Then we capture a planar scene from different depths to correct the distance error that is shown to be dependent not only on the distance but also on the pixel location. The range error profiles along the calibrated distance are classified according to their wiggling shapes and each cluster of profiles with similar shape are separately estimated using a B-spline function. The standard deviation of the remaining random noise is recorded as an uncertainty information of distance measurements. We show the performance of our calibration method quantitatively and qualitatively on various datasets, and validate the impact of our method by demonstrating an RGB-D shape refinement application.