An on-demand cleanup application running locally removes malware and its effects from a computer system. A virus scan engine scans the computer system to identify any malicious files. A system information collector tool executes to create a log file containing detailed information about the computer system and the location of all files. Identified malicious files are matched against the log file to determine the extent of the infection by the malicious files. Computer code is generated using a blank cleanup template to automatically delete the malicious files and their effects in the computer system and placed into a final cleanup template. The cleanup template is executed by a cleanup engine in order to remove the malware and its effects from the computer. A CRC tool is used to positively identify files that are to be deleted.