Abstract: During a bootstrapping process, path names of necessary bootstrap modules are collected and stored into a file. When an infected bootstrap component is detected, the method initiates emulation of the bootstrapping process within a virtual machine rather than directly cleaning malware from the infected bootstrap component. A settings file is copied into the virtual machine indicating the necessary bootstrap components in the host computer (including the infected component). Alternatively, the actual components are copied into the virtual machine. A clean version of the infected bootstrap component is made available to the virtual machine. The virtual machine is launched using the bootstrap components (including the clean version of the infected bootstrap component) and it emulates the bootstrapping process of the operating system. A successful bootstrap indicates the infected bootstrap component may be cleaned on the host computer.