An instrument cassette (100) for handling instruments (111) comprises support structures (101) for mechanically supporting the instruments (111), and a shielding structure (102, 103) for containing operational portions (112) of the instruments (111) so that a risk of unintentional touching the operational portions (112) is reduced. At least one wall (104) of the shielding structure (103) comprises channels (105) for allowing liquid and gaseous substances to flow through the wall. The substances may comprise for example hot vapor used in an autoclaving sterilization process. The channels (105) are shaped to prevent the operational portions (112) of the instruments (111) from protruding through the wall (104) via the channels (105). Thus, there is no need for a high number of very small channels which may be difficult to manufacture in a cost effective way.