New structural materials, such as carbon fiber reinforced plastic (CFRP), are used in modern machine tools for energy efficiency improvement by weight reduction. Furthermore, CFRP can manipulate thermal expansion with the fiber orientation, and this is expected to reduce thermal errors. In this research, the machining accuracy of CFRP-structured machine tools was investigated. A novel machining-based thermal error analysis was performed by cutting a test piece at specific intervals, assuming a long operation time including idle time. By measuring the geometric errors of the machined test piece, the thermal errors and the effectiveness of the CFRP application were evaluated. It was observed that CFRP-structured machine tools lead to the suppression of thermal errors, although the behavior of thermal deformation indicates mechanical anisotropy in comparison with a conventional machine tool.