A medical instrument holder assembly comprises a holder module base including first tubes defining first passages, each first passage having open upper and lower ends, at least one first web connecting and supporting those first tubes in parallel spaced-apart relation so that a fluid can circulate around and between the first tubes, and instrument supports underlying the first tubes for supporting medical instruments placed in the first passages while allowing a fluid to circulate through those passages. The holder assembly also includes a cover for seating on the base and covering the instruments supported thereby, the cover being formed by second tubes defining second instrument receiving passages, each second passage having upper and lower open ends, the lower ends having the same cross-sections as the upper ends of the first passages. At least one second web connects and supports the second tubes in parallel spaced-apart relation so that when the cover is seated on the base, the corresponding first and second passages are co-linear. Preferably, the assembly also includes an outer sterilization/storage case for containing a plurality of covered holder module bases packed closely together and a presentation tray capable of supporting a plurality of the holder module bases so that the instruments therein can be grasped easily by a surgeon.