Traffic matrix, which is required as an input of traffic engineering (TE) methods, is difficult to be obtained directly. One possible approach to obtaining the traffic matrix is to estimate it from the limited information such as link utilizations. However, estimated traffic matrix includes estimation errors which degrade the performance of TE significantly. In this paper, we propose VNT reconfiguration and traffic matrix estimation methods that reduce estimation errors while reconfiguring the VNT by cooperating with each other. Our method reconfigures the VNT gradually by dividing it into multiple stages and limiting the number of optical layer paths reconfigured in each stage. By dividing the VNT reconfiguration into multiple stages, our traffic matrix estimation method calibrates and reduces the estimation errors in each stage by using information monitored in prior stages. In addition, by limiting the number of optical layer paths reconfigured in each stage, our method avoids mista...