I left ESS running a virus scan overnight and at about 33% it found a threat in my temp folder (a setup file with a toolbar). A popup was shown and the scan completly stopped (which sucks ). As far as I know the available options regarding cleaning are: - Do not clean Infected files will not be cleaned automatically. The program will show up a warning window and allow the user to choose an action. - Default level The program will attempt to automatically clean or delete an infected file. If it is not possible to select the correct action automatically, the program offers a selection of follow-up actions. The same happens if a predefined action couldn’t be completed. - Strict cleaning The program will clean or delete all infected files. The only exceptions are the system files. If it is not possible to clean them, the user is offered an action to take in a warning window. and all of these show popups. My suggestion: Queue the popups and allow the scan to continue.