The present disclosure provides, in certain embodiments, a system and method for generating a 3D model of a biopsy specimen. The 3D model may greatly enhance the capability to identify insufficient margins surrounding neoplastic tissue obtained through an excisional biopsy, and improve communication from a pathologist back to a surgeon and/or patient. The model provides a 3D representation of the neoplastic tissue within the specimen, thereby allowing the surgeon (or other medical personnel) to rotate and orient the model at any desired angle to identify insufficient margins and relate the location of the insufficient margins to the removal site to more accurately identify the location at which additional tissue needs to be excised. By identifying the exact location at which additional tissue needs to be excised, the surgeon is able to minimize the amount of additional tissue removed from the patient in order to achieve sufficient margins.