Physical objects typically have, at the surface, a structure that is visible at the microscopic level, known as a microstructure. This structure is usually random and unique for each physical object of particular type, which allows the identification or authentication of such object. These primitives can be used to construct anti-counterfeiting systems. The thesis contains both a theoretical and practical part. The theoretical contributions consist of models of anti-counterfeiting systems, frameworks for the evaluation and pioneers the analysis of attacks against identification and authentication systems. The practical part consists of a large-scale analysis of cardboard microstructures.