Background Computer-assisted navigation was recently introduced to aid the resection of musculoskeletal tumors. However, it has not always been possible to directly navigate the osteotomy with real-time manipulation of available surgical tools. Registration techniques vary, although most existing systems use some form of surface matching. Questions/purposes We developed and evaluated a workflow model of computer-assisted bone tumor surgery and evaluated (1) the applicability of currently available software to different bones; (2) the accuracy of the navigated excision; and (3) the accuracy of a new registration technique of fluoro-CT matching. Methods Our workflow involved detailed preoperative planning with CT-MRI image fusion, three-dimensional mapping of the tumor, and planning of the resection plane. Using the workflow model, we reviewed 15 navigation procedures in 12 patients, including four with joint-saving resections and three with custom implant reconstructions. Intraoperatively, registration was performed with either paired points and surface matching (Group 1, n = 10) or a new technique of fluoro-CT image matching (Group 2, n = 5). All osteotomies were performed under direct computer navigation. Postoperatively, each case was evaluated for histologic margin and gross measurement of the achieved surgical margin. Results The margins were free from tumor in all resected specimens. In the Group 1 procedures, the correlation between preoperative planned margins and actual achieved margins was 0.631, whereas in Group 2 procedures (fluoro-CT matching), the correlation was 0.985. Conclusions Our findings suggest computer-assisted navigation is accurate and useful for bone tumor surgery. The new registration technique using fluoro-CT matching may allow more accurate resection of margins.