A method is provided for removing at least one tissue sample from a surgical patient using a biopsy instrument. The biopsy instrument comprises an elongated piercer having a piercer lumen extending therethrough. The biopsy instrument further comprises a cutter rotatably and translationally positionable relative to the piercer. The piercer has a port for receiving and transferring the tissue portion into the piercer lumen. In one embodiment of the present invention, the method for using the biopsy instrument comprises the steps of engaging tissue in the port; translating the cutter at a first, predetermined translational speed from a first position to a second position proximal to the port; measuring the translational speed of the cutter; translating the cutter at a second, predetermined translational speed from the second position to a third position proximal to the port; translating the cutter at a third, predetermined translational speed from the third position to a fourth position distal to the port; rotating the cutter at a predetermined rotation speed; measuring the rotational speed of the cutter; and modifying the translational speed of the cutter when the rotational speed of the cutter varies from the predetermined rotational speed by more than a first, predetermined differential rotational speed.