Abstract Background Ciliated muconodular papillary tumor (CMPT) is a rare papillary nodule tumor with benign and malignant characteristics that occurs in the peripheral lung. Case presentation A 70-year-old woman who underwent right hemicolectomy for colorectal cancer (CRC; pT3N0M0, p-stage II) 2 years prior, presented with a sub-centimeter growing cavity shadow on chest computed tomography (CT), which was suspected to be a CRC metastasis. Because positron emission tomography CT suggested there was no other site suspicious of recurrence, thoracoscopic resection with preoperative pleural dye marking was planned to remove the small lesion, which seemed to be hardly palpable on CT. Immediately after pleural dye marking adjacent to the lesion using cone beam CT in the hybrid operating room, thoracoscopic wedge resection was performed and the tumor was finally diagnosed as CMPT, characterized by the papillary growth of mucus-producing cells in the alveoli. Conclusion We resected the non-palpable small lung lesions following preoperative marking using cone-beam CT in the hybrid operating room. This case highlights a rare cavitary CT image of a CMPT mimicking a metastatic lung tumor from colorectal cancer.