A set of algorithms has been developed and applied, in order to quantify the morphology of structures produced by our work on computer simulation of cancellous bone remodelling. The set of algorithms is organised in three themes, based on the set of metrics they compute. The first one deals with the direct derivation of basic metrics such as the trabecular thickness, separation and number. The second deals with the area/volume distribution of bone and marrow, while the third one considers surface roughness and perimeter/area. The algorithms were tested on sample sections of cancellous bone and applied to a simulation of strain adaptation incorporating complex multi-axial loading. The metrics have shown to be independent of structural anisotropy, in contrast to some established methods that assume certain morphologies.