Systems and methods for scanning files for pestware on a protected computer are described. In one variation, locations of each of a plurality of files in a file storage device of the protected computer are identified while substantially circumventing an operating system of the protected computer. Information from each of the plurality of files is retrieved and analyzed so as to determine whether any of the plurality of files are potential pestware files. In variations, the operating system is circumvented while the information from each of the plurality of files is retrieved. In other variations, before information is retrieved from each of the plurality of files, a listing of the plurality of files is sorted according to the locations of the files on the storage device so as to reduce, even further, the time required to access the plurality of files.