A shape model generation method or system for generating a shape model from shape description data such as X-ray CT data, including a process by virtual probe measuring unit of causing a virtual probe defined as an area having a finite expansion in a virtual space in the shape description data to sequentially scan a plurality of probe paths sequentially set by probe path setting unit, measuring the shape description data and thereby acquiring a characteristic value specific to the position in the virtual space of the virtual probe for each of the probe paths and a process by the probe path setting unit of generating a new probe path using the characteristic value obtained for the probe paths and thereby sequentially setting the plurality of probe paths.