A vacuum system for removal of debris in the form of shavings, particles, or the like has been developed for use inside of a cryostat to evacuate and collect such material as it is generated during specimen preparation using a microtome, also inside of the cryostat. The system includes a vacuum assembly unit containing a vacuum collection nozzle having a suction duct. The cold assembly unit is moveably positioned adjacent to the microtome knife so that debris is suctioned away and removed concurrent with or immediately after its production during cryotomy, and is captured in a cold primary filter. The frozen debris does not melt, but remains rigid while it freeze-dries and is trapped on the filter as cold air flows over and through it, thereby maintaining the collected waste material in a very porous state. This porosity permits the collection of a large volume of debris without clogging the cold filter, in contrast to the rapid clogging which occurs when such frozen debris melts, is suctioned into, collapses within, dries and seals off the pores of a warm filter. When required, the collection nozzle and attached assembly unit can be moveably positioned out of the way of the microtome knife. The system may also include a second bacteriological filter inside or outside of the cryostat to entrap any small quantities of fine debris which may pass through the primary filter after suctioning. When necessary, both types of filters can be efficiently, economically, and safely replaced and discarded.