A biopsy system has a cutter defining a cutter lumen along an axis. One conduit in the system is configured to provide fluid communication along the cutter lumen axis; while another conduit in the system is configured to provide fluid communication lateral to the cutter lumen axis. The system may be operated in a variety of modes, including a sample cycle, a clear probe cycle, a cutter positioning cycle, an aspirate cycle, and a maintenance vacuum pulse cycle. The operational modes are selectable by a user. Depending on the mode selected by the user, the communication of vacuum, saline, or atmospheric air through the conduits, or the sealing of the conduits, will vary as a function of the axial position of the cutter.