A method and system for detecting and removing a hidden pestware file is described. One illustrative embodiment detects, using direct drive access, a file on a computer storage device; determines whether the file is also detectable by the operating system by attempting to access the file using a standard file Application-Program-Interface (API) function call of the operating system; identifies the file as a potential hidden pestware file, when the file is undetectable by the operating system; confirms through an automated pestware-signature scan of the potential hidden pestware file that the potential hidden pestware file is a hidden pestware file; and removes automatically, using direct drive access, the hidden pestware file from the storage device.