In the framework of the European Union funded research project STRATFEED for detection and identification of animal proteins in feeds, the microscopic method was optimized at several key steps and better documented. A check list was developed for uniform reporting. Characters of bone fragments, hairs, muscles and gills are fully documented. A so-called muscle ratio has been developed for the identification of muscle fibers at the level of vertebrate classes (mammals, birds and fishes). Both the improved protocol and the entire range of characters which can be observed, are documented in a Decision Support System called ARIES (Animal Remains Identification and Evaluation System). A second internet-based system called STRATFEED-DSS exclusively assists in identification of animal particles in feeds. A new strategy with microscopy as screening technique and either DNA or protein identification as confirmation technique is proposed. The advantages of this combination are the extremely low level of false negatives, low detection limits and the heat-resistant nature of microscopic detection, together with the possibility of a very specific identification of particles by one of the other methods.