The preferred embodiments are directed to a method of operating an SPM including providing probe cassette for a scanning probe microscope that includes a base having at least one probe storage receptacle, a lid mountable on the base with the probe storage receptacle at least substantially covering the at least one receptacle, and a probe retainer that retains a probe device of the scanning probe microscope in the receptacle under a compressive force. The probe cassette can be pre-loaded and shipped to a user site where the cassette can be loaded in an AFM without manual manipulation of the individual probe devices.