Of the wide variety of existing optical techniques for non-contact 3D surface mapping, Fourier Transform Interferometry (FTI) is the method that most elegantly combines simplicity with high speed and high resolution. FTI generates continuous-phase surface maps from a projected optical interference pattern, which is generated with a simple double-pinhole source and collected in a single snapshot using conventional digital camera technology. For enhanced stability and reduced system size, the fringe source can be made from a fiber optic coupler. Unfortunately, many applications require mapping of surfaces that contain challenging features not ideally suited for reconstruction using FTI. Rough and discontinuous surfaces, commonly seen in applications requiring imaging of rock particles, present a unique set of obstacles that cannot be overcome using existing FTI techniques. This work is based on an original analysis of the limitations of FTI and the means in which errors are generated by the particular features encountered in the aggregate mapping application. Several innovative solutions have been developed to enable the use of FTI on rough and discontinuous surfaces. Through filter optimization and development of a novel phase unwrapping and referencing technique, the Method of Multiple References (MoMR), this work has enabled surface error correction and simultaneous imaging of multiple particles using FTI. A complete aggregate profilometry system has been constructed, including a MoMR-FTI software package and graphical user interface, to implement these concepts. The system achieves better than 22µm z-axis resolution, and comprehensive testing has proven it capable to handle a wide variety of particle surfaces. A range of additional features have been developed, such as error correction, particle boundary mapping, and automatic data quality windowing, to enhance the usefulness of the system in its intended application. Because of its high accuracy, high speed and ability to map varied particles, the developed system is ideally suited for large-scale aggregate characterization in highway research laboratories. Additionally, the techniques developed in this work are potentially useful in a large number of applications in which surface roughness or discontinuities pose a challenge. / Ph. D.