As a serious, prevalent, and potentially fatal condition, deep venous thrombosis (DVT) results in a huge healthcare-related and socioeconomic burden. On the other hand, the placement of an inferior vena cava (IVC) filter is one of the last options to prevent the most dangerous complication of DVT, pulmonary embolism (PE). The patient was a 35-year-old man admitted to the hospital for dyspnea on exertion (NYHA class II) and lower extremity swelling. He had a history of pin implantation in his right leg and a recent history of DVT in his left calf and thigh, which was treated with warfarin. The patient was diagnosed with PE using CT angiography and was scheduled for IVC filter placement regarding the development of PE despite receiving warfarin therapy with a suitable INR. While inserting the IVC filter below the right renal vein, its legs did not fully open, and it did not go further. Thus, the procedure was terminated due to the risk of IVC perforation, and CT venography was requested, revealing the May-Thurner syndrome and a web-like, elongated filling defect attached to the anterior IVC wall, which was an old recanalized thrombosis. Considering the anatomical disorders, we decided to retrieve the IVC filter, and the warfarin dose was increased. The present report provides a rare case of IVC anomaly management during IVC filter placement. It is recommended to look for IVC anomalies when planning interventions related to this area.