BACKGROUND: Maximal safe resection is the paramount objective in the surgical management of malignant brain tumors. It is facilitated through use of image-guided neuronavigation. Intraoperative image guidance systems use preoperative magnetic resonance imaging (MRI) as the navigational map. The accuracy of neuronavigation is limited by intraoperative brain shift and can become less accurate over the course of the procedure. Intraoperative MRI can compensate for dynamic brain shift but requires significant space and capital investment, often unavailable at many centers. OBSERVATIONS: The authors described a case in which an image fusion algorithm was used in conjunction with an intraoperative computed tomography (CT) system to compensate for brain shift during resection of a brainstem hemorrhagic melanoma metastasis. Following initial debulking of the hemorrhagic metastasis, intraoperative CT was performed to ascertain extent of resection. An elastic image fusion (EIF) algorithm was used to create virtual MRI relative to both the intraoperative CT scan and preoperative MRI, which facilitated complete resection of the tumor while preserving critical brainstem anatomy. LESSONS: EIF algorithms can be used with multimodal images (preoperative MRI and intraoperative CT) and create an updated virtual MRI data set to compensate for brain shift in neurosurgery and aid in maximum safe resection of malignant brain tumors.