A microtome (100, 700, 800, 900, 1000), configured to be installed within a scanning electron microscope having a beam axis and for removing a thin portion of the top of a sample (136, 702, 804, 914, 1014), wherein the microtome (100, 700, 800, 900, 1000) comprises: a base plate; a pedestal (134, 704) coupled to the base plate such that the pedestal (134, 704) can be moved from an imaging location on the beam axis to a cutting location off the beam axis, wherein the pedestal (134, 704) has an exposed surface on which the sample (136, 702, 804, 914, 1014) can be mounted; a blade (116, 908, 1008) coupled to the base plate such that a blade location with respect to the base plate can be adjusted by moving the blade (116, 908, 1008) in a direction perpendicular to the exposed surface of the pedestal (134, 704), and parallel to the beam axis, when the pedestal (134, 704) is in the imaging location, to selectively vary a distance between the blade (116, 908, 1008) and the base plate, wherein the blade (116, 908, 1008) is further coupled to an actuator (110, 906, 1006) which moves the blade (116, 908, 1008), and wherein the actuator (110, 906, 1006) is configured to receive a control signal to direct movement of the blade (116, 908, 1008); a sensor coupled to the actuator (110, 906, 1006) and configured to produce an output signal indicating the blade location with respect to the base plate; and a computer program configured to receive the output signal from the sensor, generate the control signal based at least in part on the output signal from the sensor, and transmit the control signal to the actuator (110, 906, 1006), wherein the cutting location is closer to the blade (116, 908, 1008) than the imaging location. a base plate; a pedestal (134, 704) coupled to the base plate such that the pedestal (134, 704) can be moved from an imaging location on the beam axis to a cutting location off the beam axis, wherein the pedestal (134, 704) has an exposed surface on which the sample (136, 702, 804, 914, 1014) can be mounted; a blade (116, 908, 1008) coupled to the base plate such that a blade location with respect to the base plate can be adjusted by moving the blade (116, 908, 1008) in a direction perpendicular to the exposed surface of the pedestal (134, 704), and parallel to the beam axis, when the pedestal (134, 704) is in the imaging location, to selectively vary a distance between the blade (116, 908, 1008) and the base plate, wherein the blade (116, 908, 1008) is further coupled to an actuator (110, 906, 1006) which moves the blade (116, 908, 1008), and wherein the actuator (110, 906, 1006) is configured to receive a control signal to direct movement of the blade (116, 908, 1008); a sensor coupled to the actuator (110, 906, 1006) and configured to produce an output signal indicating the blade location with respect to the base plate; and a computer program configured to receive the output signal from the sensor, generate the control signal based at least in part on the output signal from the sensor, and transmit the control signal to the actuator (110, 906, 1006), wherein the cutting location is closer to the blade (116, 908, 1008) than the imaging location.