The inventions relate generally to protection of computing systems by isolating intrusive attacks into layers, those layers containing at least file objects and being accessible to applications, those layers further maintaining potentially intrusive file objects separately from regular file system objects such that the regular objects are protected and undisturbed. Also disclosed herein are computing systems which use layers and/or isolation layers, and various systems and methods for using those systems. Detailed information on various example embodiments of the inventions are provided in the Detailed Description below, and the inventions are defined by the appended claims.