A system and method for determining whether one or more applications in a virtual software layer and one or more applications in a base environment are compatible. The method includes intercepting an access attempt from an application on a computer system to a file on the computer system, such as a system file. The system then determines a first compatibility checking mode and whether a second version of the file exists in a virtual software layer. In response to these determinations and to intercepting the access attempt, the system attempts to perform the access using the second version of the file.