Free form surface measurement and its subsequent analysis is becoming a subject of considerable interest, not only within the engineering field, but also in bioengineering, medical and dental research. In particular, within the field of dental research, the oral structures comprise a variety of complex free form surfaces, which are often recorded by elastomeric impression materials. In this study, an optical triangulation-based, noncontact probe fitted onto a Co-ordinate Measuring Machine was used to acquire three-dimensional co-ordinate data from such complex free form surfaces. When using an optical probe to digitise a complex free form surface represented by impressions, an optimal digitisation strategy is critical to limit the uncertainty of the data acquisition procedure, because the raw data are the basis for later surface measurement and analysis. This study attempted to optimise a method for three dimensional free form surface data acquisition, measurement and analysis. A theoretical and systematic analysis of error distribution was carried out using standard objects and optimal digitisation strategies were proposed in relation to specified models. Two simulation models of two typical human tooth surfaces were extensively analysed and evaluated. Three reference systems were developed for comparative measurements of those surfaces that have fewer geometrical features. An integrated automatic data acquisition procedure was also developed to scan a large number of impressions. Several successful research applications have been carried out using the methodology developed in this study.