The system includes a biopsy needle assembly (100) for excising a tissue specimen, and includes a mandrel (102) with a core bed (116) forming a projection (122) for marking the specimen. The projection can include a marking agent for marking the specimen. An actuator assembly (200) used with needle assembly (100) includes a counter assembly (352) identifying the biopsy specimen during a procedure, and tracking the cumulative biopsies taken with the actuator. A three-dimensional biopsy mapping and focal therapy system (1102) uses an imaging system to generate and store a three-dimensional image (1472) of a target tissue. Biopsy site location and needle orientation are generated and stored with the three-dimensional image. Lesion sites of the biopsied tissue specimens are recorded with the three-dimensional image. Tumor volume is calculated and represented with the three-dimensional image. The three dimensional image is used to provide localized therapy to the diseased tissue.
