How to remove CleanThis Boot to Safe Mode with Command Prompt. In the Command Prompt window, type explorer.exe and then press Enter. Run regedit, navigate to HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\Winlogon Note the location of the file pointed to by the Shell key, delete the key, delete the actual file, and remove the startup command from the Sys Config Utility (msconfig).